https://wiki.pymol.org/api.php?action=feedcontributions&feedformat=atom&user=HsteinbePyMOL Wiki - User contributions [en]2026-05-25T03:38:44ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Surface&diff=5662Surface2011-06-22T17:17:03Z<p>Hsteinbe: </p>
<hr />
<div>The surface representation of a protein, in PyMol, shows the [http://en.wikipedia.org/wiki/Connolly_surface "Connolly" surface] or the surface that would be traced out by the '''surfaces''' of waters in contact with the protein at all possible positions. [[Image:Surface_ex.png|thumb|Surface Representation Example|right]]<br />
<br />
<br />
==Enabling==<br />
To enable the surface representation do<br />
show surface, SEL<br />
for any proper selection SEL.<br />
<br />
==Settings==<br />
*[[cavity_cull]]<br />
*[[surface_best]] <br />
*[[surface_negative_color]] <br />
*[[surface_carve_cutoff]] <br />
*[[surface_negative_visible]] <br />
*[[surface_carve_normal_cutoff]] <br />
*[[surface_normal]] <br />
*[[surface_carve_selection]] <br />
*[[surface_optimize_subsets]] <br />
*[[surface_carve_state]] <br />
*[[surface_poor]] <br />
*[[surface_circumscribe]] <br />
*[[surface_proximity]] <br />
*[[surface_clear_cutoff]] <br />
*[[surface_quality]] <br />
*[[surface_clear_selection]] <br />
*[[surface_ramp_above_mode]] <br />
*[[surface_clear_state]] <br />
*[[surface_solvent]] <br />
*[[surface_color]] <br />
*[[surface_trim_cutoff]] <br />
*[[surface_debug]] <br />
*[[surface_trim_factor]] <br />
*[[surface_miserable]] <br />
*[[surface_type]] <br />
*[[surface_mode]] <br />
<br />
===Examples===<br />
====Transparency====<br />
To adjust the transparency of surfaces try:<br />
<source lang="python"><br />
set transparency, 0.5<br />
</source><br />
Where 1.0 will be an invisible and 0.0 a completely solid surface.<br />
<br />
====Quality====<br />
To smooth your surface representation try:<br />
<source lang="python"><br />
set surface_quality, 1<br />
</source><br />
or higher if you wish, though it will take longer and might look odd.<br />
<br />
====Probe Radius====<br />
To change the probe radius other than default 1.4 Å, you need to change the solvent radius, say, 1.6 Å:<br />
<source lang="python"><br />
set solvent_radius, 1.6<br />
</source><br />
If the surface does not change correspondingly, use:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
==Tips==<br />
<br />
=== Exporting Surface/Mesh Coordinates to File===<br />
<br />
PyMOL can export its coordinates as WRL wireframe model files for VRML input.<br />
<br />
====Older PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to povray<br />
open("surface.inc","w").write(cmd.get_povray()[1])<br />
</source><br />
<br />
====Newer PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to .wrl file<br />
save myscene.wrl<br />
</source><br />
or<br />
<source lang="python"><br />
# export the coordinates to .obj file<br />
save myscene.obj<br />
</source><br />
<br />
===Representation-independent Color Control===<br />
To color the surface representation a different color than the underlying cartoon or ligand representations, simply duplicate the object, show only the surface in the duplicate, and show only the cartoon and/or ligands in the original object.<br />
<br />
Or use the [[surface_color]] setting that is available.<br />
<br />
<br />
<br />
[[Image:Representation independent color control.jpg|thumb|Representation-independent Color Control Example|left]]<br />
<br />
===Displaying a protein as surface with a ligand as sticks===<br />
An easy way to do this is to create separate objects for each type of display. <br />
<br />
1 Load your protein<br />
<br />
2 Select the ligand <br />
<br />
3 Create a separate object for the ligand <br />
<br />
4 Remove ligand atoms from the protein<br />
<br />
5 Display both objects separately<br />
<br />
Example:<br />
<source lang="python"><br />
load prot.ent,protein<br />
select ligand,resn FAD<br />
create lig_sticks,ligand<br />
remove ligand<br />
show sticks,lig_sticks<br />
show surface,protein<br />
</source><br />
<br />
<br />
Even easier is to:<br />
<br />
1 Load the protein<br />
<br />
2 S (Show) > organic > stick<br />
<br />
3 S (Show) > surface<br />
<br />
===Calculating a partial surface===<br />
There is, until now, an undocumented way to calculate a surface for only a part of an object without creating a new one:<br />
<source lang="python"><br />
flag ignore, not A/49-63/, set<br />
delete indicate<br />
show surface<br />
</source><br />
If the surface was already computed, then you'll also need to issue the command:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
See [[Get_Area]] for more information on surface area calculations.<br />
<br />
===Displaying surface inside a molecule===<br />
As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is:<br />
<source lang="python"><br />
set ambient=0<br />
set direct=0.7<br />
set reflect=0.0<br />
set backface_cull=0<br />
</source><br />
Which gives no shadows and only a few artifacts.<br />
<br />
As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray".<br />
<source lang="python"><br />
util.ray_shadows("heavy")<br />
set two_sided_lighting=1<br />
set backface_cull=0<br />
</source><br />
<br />
===Creating a Closed Surface===<br />
<gallery><br />
Image:Surface_open.png|Example OPEN Surface<br />
Image:Surface_closed.png|Example CLOSED Surface<br />
</gallery><br />
<br />
To create what I'll call a '''closed surface''' (see images), you need to first make your atom selections, then create a new object for that selection then show the surface for that object. Here's an example.<br />
<source lang="python"><br />
sel A, id 1-100<br />
create B, A<br />
show surface, B<br />
</source><br />
<br />
===Smooth surface quick (blob)===<br />
To get a quick blob type surface (not as accurate):<br />
<source lang="python"><br />
set solvent_radius, 4 <br />
alter all, vdw=4 <br />
sort<br />
set surface_quality, 1<br />
</source><br />
<br />
===Smooth surface accurate (blob)===<br />
To get an accurate blob type surface:<br />
<source lang="python"><br />
set surface_quality, 1<br />
alter all, b=50<br />
alter all, q=1<br />
set gaussian_resolution,5<br />
map_new mapA, gaussian, 1, sele or pdb, 6<br />
isosurface surfA, mapA<br />
</source><br />
'''Notes:''' Set gaussian resolution is variable with a larger number causing a more smooth surface (4 is medium and 8 is very smooth).<br />
The temperature factor field (b) has at least as much impact as the resolution setting, so increasing b factors is the more computationally efficient way of increasing the blur effect.<br />
If you are displaying more then one surface in a .pse file you must create a new map for each one (if you have three you will create mapA for the first, mapB for the second and mapC for the third), then you apply an isosurface to each map (isosurface surfA, mapA - isosurface surfB, mapB - isosurface surfC, mapC).<br />
<br />
=== Huge Surfaces ===<br />
If your protein or complex is too large to render ([[ray]] runs out of RAM, for example) then check out the [[Huge_surfaces|tip for huge surfaces]].<br />
<br />
== Performance ==<br />
To optimize performance and responsiveness, PyMOL tends to defer compute-intensive tasks until their results are actually needed. Thus, <br />
<source lang="python"><br />
cmd.show("surface")<br />
</source><br />
doesn't actually show a surface, it only sets the surface visibility flag on the atoms present (for future reference). An actual surface won't be computed until PyMOL is asked to refresh or render the display. When running a script, you can force an update by calling:<br />
<source lang="python"><br />
cmd.refresh()<br />
</source><br />
after cmd.show.<br />
<br />
[[Category:Representations|Surface]]<br />
[[Category:VRML]]<br />
[[Category:Surfaces]]<br />
[[Category:Performance]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Surface&diff=5661Surface2011-06-22T17:02:11Z<p>Hsteinbe: /* Smooth surface (blob) */</p>
<hr />
<div>The surface representation of a protein, in PyMol, shows the [http://en.wikipedia.org/wiki/Connolly_surface "Connolly" surface] or the surface that would be traced out by the '''surfaces''' of waters in contact with the protein at all possible positions. [[Image:Surface_ex.png|thumb|Surface Representation Example|right]]<br />
<br />
<br />
==Enabling==<br />
To enable the surface representation do<br />
show surface, SEL<br />
for any proper selection SEL.<br />
<br />
==Settings==<br />
*[[cavity_cull]]<br />
*[[surface_best]] <br />
*[[surface_negative_color]] <br />
*[[surface_carve_cutoff]] <br />
*[[surface_negative_visible]] <br />
*[[surface_carve_normal_cutoff]] <br />
*[[surface_normal]] <br />
*[[surface_carve_selection]] <br />
*[[surface_optimize_subsets]] <br />
*[[surface_carve_state]] <br />
*[[surface_poor]] <br />
*[[surface_circumscribe]] <br />
*[[surface_proximity]] <br />
*[[surface_clear_cutoff]] <br />
*[[surface_quality]] <br />
*[[surface_clear_selection]] <br />
*[[surface_ramp_above_mode]] <br />
*[[surface_clear_state]] <br />
*[[surface_solvent]] <br />
*[[surface_color]] <br />
*[[surface_trim_cutoff]] <br />
*[[surface_debug]] <br />
*[[surface_trim_factor]] <br />
*[[surface_miserable]] <br />
*[[surface_type]] <br />
*[[surface_mode]] <br />
<br />
===Examples===<br />
====Transparency====<br />
To adjust the transparency of surfaces try:<br />
<source lang="python"><br />
set transparency, 0.5<br />
</source><br />
Where 1.0 will be an invisible and 0.0 a completely solid surface.<br />
<br />
====Quality====<br />
To smooth your surface representation try:<br />
<source lang="python"><br />
set surface_quality, 1<br />
</source><br />
or higher if you wish, though it will take longer and might look odd.<br />
<br />
====Probe Radius====<br />
To change the probe radius other than default 1.4 Å, you need to change the solvent radius, say, 1.6 Å:<br />
<source lang="python"><br />
set solvent_radius, 1.6<br />
</source><br />
If the surface does not change correspondingly, use:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
==Tips==<br />
<br />
=== Exporting Surface/Mesh Coordinates to File===<br />
<br />
PyMOL can export its coordinates as WRL wireframe model files for VRML input.<br />
<br />
====Older PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to povray<br />
open("surface.inc","w").write(cmd.get_povray()[1])<br />
</source><br />
<br />
====Newer PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to .wrl file<br />
save myscene.wrl<br />
</source><br />
or<br />
<source lang="python"><br />
# export the coordinates to .obj file<br />
save myscene.obj<br />
</source><br />
<br />
===Representation-independent Color Control===<br />
To color the surface representation a different color than the underlying cartoon or ligand representations, simply duplicate the object, show only the surface in the duplicate, and show only the cartoon and/or ligands in the original object.<br />
<br />
Or use the [[surface_color]] setting that is available.<br />
<br />
<br />
<br />
[[Image:Representation independent color control.jpg|thumb|Representation-independent Color Control Example|left]]<br />
<br />
===Displaying a protein as surface with a ligand as sticks===<br />
An easy way to do this is to create separate objects for each type of display. <br />
<br />
1 Load your protein<br />
<br />
2 Select the ligand <br />
<br />
3 Create a separate object for the ligand <br />
<br />
4 Remove ligand atoms from the protein<br />
<br />
5 Display both objects separately<br />
<br />
Example:<br />
<source lang="python"><br />
load prot.ent,protein<br />
select ligand,resn FAD<br />
create lig_sticks,ligand<br />
remove ligand<br />
show sticks,lig_sticks<br />
show surface,protein<br />
</source><br />
<br />
<br />
Even easier is to:<br />
<br />
1 Load the protein<br />
<br />
2 S (Show) > organic > stick<br />
<br />
3 S (Show) > surface<br />
<br />
===Calculating a partial surface===<br />
There is, until now, an undocumented way to calculate a surface for only a part of an object without creating a new one:<br />
<source lang="python"><br />
flag ignore, not A/49-63/, set<br />
delete indicate<br />
show surface<br />
</source><br />
If the surface was already computed, then you'll also need to issue the command:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
See [[Get_Area]] for more information on surface area calculations.<br />
<br />
===Displaying surface inside a molecule===<br />
As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is:<br />
<source lang="python"><br />
set ambient=0<br />
set direct=0.7<br />
set reflect=0.0<br />
set backface_cull=0<br />
</source><br />
Which gives no shadows and only a few artifacts.<br />
<br />
As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray".<br />
<source lang="python"><br />
util.ray_shadows("heavy")<br />
set two_sided_lighting=1<br />
set backface_cull=0<br />
</source><br />
<br />
===Creating a Closed Surface===<br />
<gallery><br />
Image:Surface_open.png|Example OPEN Surface<br />
Image:Surface_closed.png|Example CLOSED Surface<br />
</gallery><br />
<br />
To create what I'll call a '''closed surface''' (see images), you need to first make your atom selections, then create a new object for that selection then show the surface for that object. Here's an example.<br />
<source lang="python"><br />
sel A, id 1-100<br />
create B, A<br />
show surface, B<br />
</source><br />
<br />
===Smooth surface quick (blob)===<br />
To quickly get a blob type surface (not as accurate):<br />
<source lang="python"><br />
set solvent_radius, 4 <br />
alter all, vdw=4 <br />
sort<br />
set surface_quality, 1<br />
</source><br />
<br />
=== Huge Surfaces ===<br />
If your protein or complex is too large to render ([[ray]] runs out of RAM, for example) then check out the [[Huge_surfaces|tip for huge surfaces]].<br />
<br />
== Performance ==<br />
To optimize performance and responsiveness, PyMOL tends to defer compute-intensive tasks until their results are actually needed. Thus, <br />
<source lang="python"><br />
cmd.show("surface")<br />
</source><br />
doesn't actually show a surface, it only sets the surface visibility flag on the atoms present (for future reference). An actual surface won't be computed until PyMOL is asked to refresh or render the display. When running a script, you can force an update by calling:<br />
<source lang="python"><br />
cmd.refresh()<br />
</source><br />
after cmd.show.<br />
<br />
[[Category:Representations|Surface]]<br />
[[Category:VRML]]<br />
[[Category:Surfaces]]<br />
[[Category:Performance]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Surface&diff=5660Surface2011-06-22T15:28:45Z<p>Hsteinbe: </p>
<hr />
<div>The surface representation of a protein, in PyMol, shows the [http://en.wikipedia.org/wiki/Connolly_surface "Connolly" surface] or the surface that would be traced out by the '''surfaces''' of waters in contact with the protein at all possible positions. [[Image:Surface_ex.png|thumb|Surface Representation Example|right]]<br />
<br />
<br />
==Enabling==<br />
To enable the surface representation do<br />
show surface, SEL<br />
for any proper selection SEL.<br />
<br />
==Settings==<br />
*[[cavity_cull]]<br />
*[[surface_best]] <br />
*[[surface_negative_color]] <br />
*[[surface_carve_cutoff]] <br />
*[[surface_negative_visible]] <br />
*[[surface_carve_normal_cutoff]] <br />
*[[surface_normal]] <br />
*[[surface_carve_selection]] <br />
*[[surface_optimize_subsets]] <br />
*[[surface_carve_state]] <br />
*[[surface_poor]] <br />
*[[surface_circumscribe]] <br />
*[[surface_proximity]] <br />
*[[surface_clear_cutoff]] <br />
*[[surface_quality]] <br />
*[[surface_clear_selection]] <br />
*[[surface_ramp_above_mode]] <br />
*[[surface_clear_state]] <br />
*[[surface_solvent]] <br />
*[[surface_color]] <br />
*[[surface_trim_cutoff]] <br />
*[[surface_debug]] <br />
*[[surface_trim_factor]] <br />
*[[surface_miserable]] <br />
*[[surface_type]] <br />
*[[surface_mode]] <br />
<br />
===Examples===<br />
====Transparency====<br />
To adjust the transparency of surfaces try:<br />
<source lang="python"><br />
set transparency, 0.5<br />
</source><br />
Where 1.0 will be an invisible and 0.0 a completely solid surface.<br />
<br />
====Quality====<br />
To smooth your surface representation try:<br />
<source lang="python"><br />
set surface_quality, 1<br />
</source><br />
or higher if you wish, though it will take longer and might look odd.<br />
<br />
====Probe Radius====<br />
To change the probe radius other than default 1.4 Å, you need to change the solvent radius, say, 1.6 Å:<br />
<source lang="python"><br />
set solvent_radius, 1.6<br />
</source><br />
If the surface does not change correspondingly, use:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
==Tips==<br />
<br />
=== Exporting Surface/Mesh Coordinates to File===<br />
<br />
PyMOL can export its coordinates as WRL wireframe model files for VRML input.<br />
<br />
====Older PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to povray<br />
open("surface.inc","w").write(cmd.get_povray()[1])<br />
</source><br />
<br />
====Newer PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to .wrl file<br />
save myscene.wrl<br />
</source><br />
or<br />
<source lang="python"><br />
# export the coordinates to .obj file<br />
save myscene.obj<br />
</source><br />
<br />
===Representation-independent Color Control===<br />
To color the surface representation a different color than the underlying cartoon or ligand representations, simply duplicate the object, show only the surface in the duplicate, and show only the cartoon and/or ligands in the original object.<br />
<br />
Or use the [[surface_color]] setting that is available.<br />
<br />
<br />
<br />
[[Image:Representation independent color control.jpg|thumb|Representation-independent Color Control Example|left]]<br />
<br />
===Displaying a protein as surface with a ligand as sticks===<br />
An easy way to do this is to create separate objects for each type of display. <br />
<br />
1 Load your protein<br />
<br />
2 Select the ligand <br />
<br />
3 Create a separate object for the ligand <br />
<br />
4 Remove ligand atoms from the protein<br />
<br />
5 Display both objects separately<br />
<br />
Example:<br />
<source lang="python"><br />
load prot.ent,protein<br />
select ligand,resn FAD<br />
create lig_sticks,ligand<br />
remove ligand<br />
show sticks,lig_sticks<br />
show surface,protein<br />
</source><br />
<br />
<br />
Even easier is to:<br />
<br />
1 Load the protein<br />
<br />
2 S (Show) > organic > stick<br />
<br />
3 S (Show) > surface<br />
<br />
===Calculating a partial surface===<br />
There is, until now, an undocumented way to calculate a surface for only a part of an object without creating a new one:<br />
<source lang="python"><br />
flag ignore, not A/49-63/, set<br />
delete indicate<br />
show surface<br />
</source><br />
If the surface was already computed, then you'll also need to issue the command:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
See [[Get_Area]] for more information on surface area calculations.<br />
<br />
===Displaying surface inside a molecule===<br />
As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is:<br />
<source lang="python"><br />
set ambient=0<br />
set direct=0.7<br />
set reflect=0.0<br />
set backface_cull=0<br />
</source><br />
Which gives no shadows and only a few artifacts.<br />
<br />
As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray".<br />
<source lang="python"><br />
util.ray_shadows("heavy")<br />
set two_sided_lighting=1<br />
set backface_cull=0<br />
</source><br />
<br />
===Creating a Closed Surface===<br />
<gallery><br />
Image:Surface_open.png|Example OPEN Surface<br />
Image:Surface_closed.png|Example CLOSED Surface<br />
</gallery><br />
<br />
To create what I'll call a '''closed surface''' (see images), you need to first make your atom selections, then create a new object for that selection then show the surface for that object. Here's an example.<br />
<source lang="python"><br />
sel A, id 1-100<br />
create B, A<br />
show surface, B<br />
</source><br />
<br />
===Smooth surface (blob)===<br />
To get a blob type surface try:<br />
<source lang="python"><br />
set solvent_radius, 4 <br />
alter all, vdw=4 <br />
sort<br />
set surface_quality, 1<br />
</source><br />
<br />
=== Huge Surfaces ===<br />
If your protein or complex is too large to render ([[ray]] runs out of RAM, for example) then check out the [[Huge_surfaces|tip for huge surfaces]].<br />
<br />
== Performance ==<br />
To optimize performance and responsiveness, PyMOL tends to defer compute-intensive tasks until their results are actually needed. Thus, <br />
<source lang="python"><br />
cmd.show("surface")<br />
</source><br />
doesn't actually show a surface, it only sets the surface visibility flag on the atoms present (for future reference). An actual surface won't be computed until PyMOL is asked to refresh or render the display. When running a script, you can force an update by calling:<br />
<source lang="python"><br />
cmd.refresh()<br />
</source><br />
after cmd.show.<br />
<br />
[[Category:Representations|Surface]]<br />
[[Category:VRML]]<br />
[[Category:Surfaces]]<br />
[[Category:Performance]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Surface&diff=5659Surface2011-06-22T15:25:15Z<p>Hsteinbe: </p>
<hr />
<div>The surface representation of a protein, in PyMol, shows the [http://en.wikipedia.org/wiki/Connolly_surface "Connolly" surface] or the surface that would be traced out by the '''surfaces''' of waters in contact with the protein at all possible positions. [[Image:Surface_ex.png|thumb|Surface Representation Example|right]]<br />
<br />
<br />
==Enabling==<br />
To enable the surface representation do<br />
show surface, SEL<br />
for any proper selection SEL.<br />
<br />
==Settings==<br />
*[[cavity_cull]]<br />
*[[surface_best]] <br />
*[[surface_negative_color]] <br />
*[[surface_carve_cutoff]] <br />
*[[surface_negative_visible]] <br />
*[[surface_carve_normal_cutoff]] <br />
*[[surface_normal]] <br />
*[[surface_carve_selection]] <br />
*[[surface_optimize_subsets]] <br />
*[[surface_carve_state]] <br />
*[[surface_poor]] <br />
*[[surface_circumscribe]] <br />
*[[surface_proximity]] <br />
*[[surface_clear_cutoff]] <br />
*[[surface_quality]] <br />
*[[surface_clear_selection]] <br />
*[[surface_ramp_above_mode]] <br />
*[[surface_clear_state]] <br />
*[[surface_solvent]] <br />
*[[surface_color]] <br />
*[[surface_trim_cutoff]] <br />
*[[surface_debug]] <br />
*[[surface_trim_factor]] <br />
*[[surface_miserable]] <br />
*[[surface_type]] <br />
*[[surface_mode]] <br />
<br />
===Examples===<br />
====Transparency====<br />
To adjust the transparency of surfaces try:<br />
<source lang="python"><br />
set transparency, 0.5<br />
</source><br />
Where 1.0 will be an invisible and 0.0 a completely solid surface.<br />
<br />
====Quality====<br />
To smooth your surface representation try:<br />
<source lang="python"><br />
set surface_quality, 1<br />
</source><br />
or higher if you wish, though it will take longer and might look odd.<br />
<br />
====Probe Radius====<br />
To change the probe radius other than default 1.4 Å, you need to change the solvent radius, say, 1.6 Å:<br />
<source lang="python"><br />
set solvent_radius, 1.6<br />
</source><br />
If the surface does not change correspondingly, use:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
==Tips==<br />
<br />
=== Exporting Surface/Mesh Coordinates to File===<br />
<br />
PyMOL can export its coordinates as WRL wireframe model files for VRML input.<br />
<br />
====Older PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to povray<br />
open("surface.inc","w").write(cmd.get_povray()[1])<br />
</source><br />
<br />
====Newer PyMOL Versions====<br />
<source lang="python"><br />
# export the coordinates to .wrl file<br />
save myscene.wrl<br />
</source><br />
or<br />
<source lang="python"><br />
# export the coordinates to .obj file<br />
save myscene.obj<br />
</source><br />
<br />
===Representation-independent Color Control===<br />
To color the surface representation a different color than the underlying cartoon or ligand representations, simply duplicate the object, show only the surface in the duplicate, and show only the cartoon and/or ligands in the original object.<br />
<br />
Or use the [[surface_color]] setting that is available.<br />
<br />
<br />
<br />
[[Image:Representation independent color control.jpg|thumb|Representation-independent Color Control Example|left]]<br />
<br />
===Displaying a protein as surface with a ligand as sticks===<br />
An easy way to do this is to create separate objects for each type of display. <br />
<br />
1 Load your protein<br />
<br />
2 Select the ligand <br />
<br />
3 Create a separate object for the ligand <br />
<br />
4 Remove ligand atoms from the protein<br />
<br />
5 Display both objects separately<br />
<br />
Example:<br />
<source lang="python"><br />
load prot.ent,protein<br />
select ligand,resn FAD<br />
create lig_sticks,ligand<br />
remove ligand<br />
show sticks,lig_sticks<br />
show surface,protein<br />
</source><br />
<br />
<br />
Even easier is to:<br />
<br />
1 Load the protein<br />
<br />
2 S (Show) > organic > stick<br />
<br />
3 S (Show) > surface<br />
<br />
===Calculating a partial surface===<br />
There is, until now, an undocumented way to calculate a surface for only a part of an object without creating a new one:<br />
<source lang="python"><br />
flag ignore, not A/49-63/, set<br />
delete indicate<br />
show surface<br />
</source><br />
If the surface was already computed, then you'll also need to issue the command:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
See [[Get_Area]] for more information on surface area calculations.<br />
<br />
===Displaying surface inside a molecule===<br />
As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is:<br />
<source lang="python"><br />
set ambient=0<br />
set direct=0.7<br />
set reflect=0.0<br />
set backface_cull=0<br />
</source><br />
Which gives no shadows and only a few artifacts.<br />
<br />
As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray".<br />
<source lang="python"><br />
util.ray_shadows("heavy")<br />
set two_sided_lighting=1<br />
set backface_cull=0<br />
</source><br />
<br />
===Creating a Closed Surface===<br />
<gallery><br />
Image:Surface_open.png|Example OPEN Surface<br />
Image:Surface_closed.png|Example CLOSED Surface<br />
</gallery><br />
<br />
To create what I'll call a '''closed surface''' (see images), you need to first make your atom selections, then create a new object for that selection then show the surface for that object. Here's an example.<br />
<source lang="python"><br />
sel A, id 1-100<br />
create B, A<br />
show surface, B<br />
</source><br />
<br />
====Smooth surface (blob)====<br />
To get a blob type surface try:<br />
<source lang="python"><br />
set solvent_radius, 4 <br />
alter all, vdw=4 <br />
sort<br />
set surface_quality, 1<br />
</source><br />
<br />
=== Huge Surfaces ===<br />
If your protein or complex is too large to render ([[ray]] runs out of RAM, for example) then check out the [[Huge_surfaces|tip for huge surfaces]].<br />
<br />
== Performance ==<br />
To optimize performance and responsiveness, PyMOL tends to defer compute-intensive tasks until their results are actually needed. Thus, <br />
<source lang="python"><br />
cmd.show("surface")<br />
</source><br />
doesn't actually show a surface, it only sets the surface visibility flag on the atoms present (for future reference). An actual surface won't be computed until PyMOL is asked to refresh or render the display. When running a script, you can force an update by calling:<br />
<source lang="python"><br />
cmd.refresh()<br />
</source><br />
after cmd.show.<br />
<br />
[[Category:Representations|Surface]]<br />
[[Category:VRML]]<br />
[[Category:Surfaces]]<br />
[[Category:Performance]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5282Covers2008-12-08T03:38:18Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.<br />
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
<br />
Image:050923_h.a.steinberg_JBC.jpg|'''GalNAc kinase''', [http://www.jbc.org/content/vol280/issue38/cover.shtml JBC], September 23, 2005 Cover, Volume 280, Issue 38.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:050923_h.a.steinberg_JBC.jpg&diff=1555File:050923 h.a.steinberg JBC.jpg2008-12-08T03:36:32Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5281Covers2008-12-08T03:34:21Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.<br />
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:050624_h.a.steinberg_jmb1.jpg&diff=1553File:050624 h.a.steinberg jmb1.jpg2008-12-08T03:31:55Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5280Covers2008-12-08T03:29:18Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.<br />
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:050624_h.a.steinberg_JMB.jpg&diff=1306File:050624 h.a.steinberg JMB.jpg2008-12-08T03:17:25Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5279Covers2008-12-08T03:15:24Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:060101_h.a.steinberg_protein_science.jpg&diff=1311File:060101 h.a.steinberg protein science.jpg2008-12-08T03:12:06Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5278Covers2008-12-08T03:09:47Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:061201_h.a.steinberg_molec_micro.jpg&diff=1560File:061201 h.a.steinberg molec micro.jpg2008-12-08T03:08:20Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5277Covers2008-12-08T03:06:03Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:061208_h.a.steinberg_molec_cell.jpg&diff=1076File:061208 h.a.steinberg molec cell.jpg2008-12-08T03:02:54Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5276Covers2008-12-08T02:59:50Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:070301_h.a.steinberg_protein_science.jpg&diff=1078File:070301 h.a.steinberg protein science.jpg2008-12-08T02:56:15Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5275Covers2008-12-08T02:53:31Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:070415.h.a.steinberg_ABB.jpg&diff=1565File:070415.h.a.steinberg ABB.jpg2008-12-08T02:45:21Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5274Covers2008-12-08T02:43:38Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], Apr. 5th, 2007.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5273Covers2008-12-08T02:35:46Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://adam.steinbergs.us/covers/ansari_biochemi_08.jpg BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], Apr. 5th, 2007.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:080701_h.a.steinberg_biochemie.jpg&diff=1090File:080701 h.a.steinberg biochemie.jpg2008-12-08T02:33:09Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5271Covers2008-12-05T18:58:26Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], Apr. 5th, 2007.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:070803_h.a.steinberg_molec_cell.jpg&diff=1080File:070803 h.a.steinberg molec cell.jpg2008-12-05T18:46:14Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5270Covers2008-12-05T18:42:57Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Number 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], Apr. 5th, 2007.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:080118_h.a.steinberg_JBC.jpg&diff=1088File:080118 h.a.steinberg JBC.jpg2008-12-05T18:38:50Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Covers&diff=5269Covers2008-12-05T18:36:00Z<p>Hsteinbe: /* PyMOL-created Journal Covers */</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_jbc_sm.gif|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Number 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Irons''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], Apr. 5th, 2007.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
</gallery></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:080118_h.a.steinberg_jbc_sm.gif&diff=1328File:080118 h.a.steinberg jbc sm.gif2008-12-05T18:31:49Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:H.a.steinberg_JBC_08.jpg&diff=1836File:H.a.steinberg JBC 08.jpg2008-12-05T18:27:37Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=File:H.a.steinberg_jbc_08_sm.gif&diff=2088File:H.a.steinberg jbc 08 sm.gif2008-12-05T18:26:46Z<p>Hsteinbe: </p>
<hr />
<div></div>Hsteinbehttps://wiki.pymol.org/index.php?title=Color&diff=5177Color2007-03-22T14:54:46Z<p>Hsteinbe: /* EXAMPLES */</p>
<hr />
<div>===DESCRIPTION===<br />
'''color''' changes the color of an object or an atom selection.<br />
<br />
===USAGE===<br />
color color-name<br />
color color-name, object-name<br />
color color-name, (selection)<br />
<br />
===PYMOL API===<br />
<source lang="python">cmd.color( string color, string selection )</source><br />
<br />
==Using RGB for Color==<br />
If you prefer RGB to color any object<br />
<source lang="python"><br />
set_color newcolor, [r,g,b]<br />
color newcolor<br />
</source><br />
List of [[Color Values]]<br />
<br />
==EXAMPLES==<br />
===Color all carbons yellow===<br />
<source lang="python">color yellow, (name C*)</source><br />
<br />
===RGB Example===<br />
<source lang="python"><br />
set_color khaki, [195,176,145]<br />
color khaki<br />
</source><br />
<br />
===Color by Spectrum Example===<br />
Color by spectrum is in the GUI menu but did you realize that the spectrum is not limited to a simple rainbow?<br />
<source lang="python"><br />
spectrum count, x, object_name<br />
</source><br />
x can can be anyone of the following:<br />
blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta, green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr, magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red, magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green, green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg <br />
<br />
===B-Factors===<br />
The command to color a molecule by B-Factors (B Factors) is:<br />
<source lang="python"><br />
cmd.spectrum("b", selection="SEL");<br />
</source><br />
where '''SEL''' is a valid selection, for example, "protA and n. CA", for protein A's alpha carbons.<br />
<br />
====Reassigning B-Factors and Coloring====<br />
It is commonplace to replace the B-Factor column of a protein with some other biochemical property at that residue, observed from some calculation or experiment. PyMOL can easily reassign the B-Factors and color them, too. The following example will load a protein, set ALL it's B Factors to "0", read in a list of properties for each alpha carbon in the proteins, assign those new values as the B-Factor values and color by the new values. This example is possible because commands PyMOL does not recognize are passed to the Python interpreter --- a very powerful tool.<br />
<source lang="python"><br />
# load the protein<br />
cmd.load("protA.pdb")<br />
<br />
# open the file of new values (just 1 column of numbers, one for each alpha carbon)<br />
inFile = open("newBFactors", 'r')<br />
<br />
# create the global, stored array<br />
stored.newB = []<br />
<br />
# read the new B factors from file<br />
for line in inFile.readlines(): stored.newB.append( float(line) )<br />
<br />
# close the input file<br />
inFile.close()<br />
<br />
# clear out the old B Factors<br />
alter protA, b=0.0<br />
<br />
# update the B Factors with new properties<br />
alter protA and n. CA, b=stored.newB.pop(0)<br />
<br />
# color the protein based on the new B Factors of the alpha carbons<br />
cmd.spectrum("b", "protA and n. CA")<br />
</source><br />
<br />
If you want to save the file with the new B Factor values for each alpha carbon,<br />
<source lang="python"><br />
cmd.save("protA_newBFactors.pdb", "protA")<br />
</source><br />
or similar is all you need.<br />
<br />
<br />
[[Category:Objects_and_Selections]]<br />
[[Category:Commands|color]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Color_Values&diff=3440Color Values2007-03-22T14:36:14Z<p>Hsteinbe: </p>
<hr />
<div>==Background==<br />
*Naming<br />
**All listed colours can be specified by name (eg color red, mymolecule)<br />
**American and English spellings of gray/grey and color/colour can be used<br />
*Sources<br />
**Pymol colours are specified as triples of independent Red, Green and Blue contribution in range 0-1.0<br />
**Colour specs from source files Color.c, menu.py and appearance.py of Pymol 0.99 beta29<br />
**Colour names can be defined/redefined using set_color command or interactively in Colors item within Setting menu<br />
==Spectral range colours==<br />
Spectral ranges are available by name including numerical value (eg grey56, s532)<br />
*Grays from 'gray00' to 'gray99' (white to black)<br />
*Spectrum from 's000' to 's999' (violet to red)<br />
*Original spectrum with extra blue and red at ends from 'o000' to 'o999'<br />
*Reversed offset spectrum from 'r000' to 'r999'<br />
*Complementary spectrum from 'c000' to 'c999'<br />
*Complementary spectrum separated by white from 'w000' to 'w999'<br />
See Colour.c in source code for details about how spectra are calculated<br />
==Simple named colours==<br />
{| cellpadding="1"<br />
|- align="center"<br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||bgcolor=gray|note<br />
|- align="center"<br />
|bgcolor="#7fffff"|&nbsp;||aquamarine||0.5||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#000000"|&nbsp;||black||0.0||0.0||0.0||<br />
|- align="center"<br />
|bgcolor="#0000ff"|&nbsp;||blue||0.0||0.0||1.0||<br />
|- align="center"<br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite||0.85||0.85||1.00||<br />
|- align="center"<br />
|bgcolor="#1919ff"|&nbsp;||br0||0.1||0.1||1.0||<br />
|- align="center"<br />
|bgcolor="#3319e5"|&nbsp;||br1||0.2||0.1||0.9||<br />
|- align="center"<br />
|bgcolor="#4c19cc"|&nbsp;||br2||0.3||0.1||0.8||<br />
|- align="center"<br />
|bgcolor="#6619b2"|&nbsp;||br3||0.4||0.1||0.7||<br />
|- align="center"<br />
|bgcolor="#7f1999"|&nbsp;||br4||0.5||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#99197f"|&nbsp;||br5||0.6||0.1||0.5||<br />
|- align="center"<br />
|bgcolor="#b21966"|&nbsp;||br6||0.7||0.1||0.4||<br />
|- align="center"<br />
|bgcolor="#cc194c"|&nbsp;||br7||0.8||0.1||0.3||<br />
|- align="center"<br />
|bgcolor="#e51933"|&nbsp;||br8||0.9||0.1||0.2||<br />
|- align="center"<br />
|bgcolor="#ff1919"|&nbsp;||br9||1.0||0.1||0.1||<br />
|- align="center"<br />
|bgcolor="#ffb233"|&nbsp;||brightorange||1.0||0.7||0.2||<br />
|- align="center"<br />
|bgcolor="#a5512b"|&nbsp;||brown||0.65||0.32||0.17||<br />
|- align="center"<br />
|bgcolor="#33ff33"|&nbsp;||carbon||0.2||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#7fff00"|&nbsp;||chartreuse||0.5||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#8d381c"|&nbsp;||chocolate||0.555||0.222||0.111||<br />
|- align="center"<br />
|bgcolor="#00ffff"|&nbsp;||cyan||0.0||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon||0.73||0.55||0.52||<br />
|- align="center"<br />
|bgcolor="#ffff00"|&nbsp;||dash||1.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue||0.25||0.25||0.65||deep<br />
|- align="center"<br />
|bgcolor="#999919"|&nbsp;||deepolive||0.6||0.6||0.1||<br />
|- align="center"<br />
|bgcolor="#991999"|&nbsp;||deeppurple||0.6||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#ff7f7f"|&nbsp;||deepsalmon||1.0||0.5||0.5||duplicated?<br />
|- align="center"<br />
|bgcolor="#ff6b6b"|&nbsp;||deepsalmon||1.00||0.42||0.42||duplicated?<br />
|- align="center"<br />
|bgcolor="#199999"|&nbsp;||deepteal||0.1||0.6||0.6||<br />
|- align="center"<br />
|bgcolor="#191999"|&nbsp;||density||0.1||0.1||0.6||<br />
|- align="center"<br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet||0.70||0.50||0.50||<br />
|- align="center"<br />
|bgcolor="#b12121"|&nbsp;||firebrick||0.698||0.13||0.13||<br />
|- align="center"<br />
|bgcolor="#339933"|&nbsp;||forest||0.2||0.6||0.2||<br />
|- align="center"<br />
|bgcolor="#7f7f7f"|&nbsp;||gray||0.5||0.5||0.5||american spelling<br />
|- align="center"<br />
|bgcolor="#00ff00"|&nbsp;||green||0.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#3fffbf"|&nbsp;||greencyan||0.25||1.00||0.75||<br />
|- align="center"<br />
|bgcolor="#7f7f7f"|&nbsp;||grey||0.5||0.5||0.5||english spelling<br />
|- align="center"<br />
|bgcolor="#ff007f"|&nbsp;||hotpink||1.0||0.0||0.5||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||hydrogen||0.9||0.9||0.9||<br />
|- align="center"<br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center"<br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta||1.0||0.2||0.8||<br />
|- align="center"<br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center"<br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center"<br />
|bgcolor="#66b2b2"|&nbsp;||lightteal||0.4||0.7||0.7||<br />
|- align="center"<br />
|bgcolor="#7fff7f"|&nbsp;||lime||0.5||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#00ff7f"|&nbsp;||limegreen||0.0||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center"<br />
|bgcolor="#ff00ff"|&nbsp;||magenta||1.0||0.0||1.0||<br />
|- align="center"<br />
|bgcolor="#007fff"|&nbsp;||marine||0.0||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#3333ff"|&nbsp;||nitrogen||0.2||0.2||1.0||<br />
|- align="center"<br />
|bgcolor="#c4b200"|&nbsp;||olive||0.77||0.70||0.00||<br />
|- align="center"<br />
|bgcolor="#ff7f00"|&nbsp;||orange||1.0||0.5||0.0||<br />
|- align="center"<br />
|bgcolor="#ff4c4c"|&nbsp;||oxygen||1.0||0.3||0.3||<br />
|- align="center"<br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center"<br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center"<br />
|bgcolor="#ffa5d8"|&nbsp;||pink||1.0||0.65||0.85||<br />
|- align="center"<br />
|bgcolor="#bf00bf"|&nbsp;||purple||0.75||0.00||0.75||<br />
|- align="center"<br />
|bgcolor="#7f00ff"|&nbsp;||purpleblue||0.5||0.0||1.0||legacy name<br />
|- align="center"<br />
|bgcolor="#b24c66"|&nbsp;||raspberry||0.70||0.30||0.40||<br />
|- align="center"<br />
|bgcolor="#ff0000"|&nbsp;||red||1.0||0.0||0.0||<br />
|- align="center"<br />
|bgcolor="#993333"|&nbsp;||ruby||0.6||0.2||0.2||<br />
|- align="center"<br />
|bgcolor="#ff9999"|&nbsp;||salmon||1.0||0.6||0.6||was 0.5<br />
|- align="center"<br />
|bgcolor="#b78c4c"|&nbsp;||sand||0.72||0.55||0.30||<br />
|- align="center"<br />
|bgcolor="#337fcc"|&nbsp;||skyblue||0.20||0.50||0.80||<br />
|- align="center"<br />
|bgcolor="#7f7fff"|&nbsp;||slate||0.5||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#8cb266"|&nbsp;||smudge||0.55||0.70||0.40||<br />
|- align="center"<br />
|bgcolor="#84bf00"|&nbsp;||splitpea||0.52||0.75||0.00||<br />
|- align="center"<br />
|bgcolor="#e5c53f"|&nbsp;||sulfur||0.9||0.775||0.25||far enough from yellow<br />
|- align="center"<br />
|bgcolor="#00bfbf"|&nbsp;||teal||0.00||0.75||0.75||<br />
|- align="center"<br />
|bgcolor="#4c4cff"|&nbsp;||tv_blue||0.3||0.3||1.0||<br />
|- align="center"<br />
|bgcolor="#33ff33"|&nbsp;||tv_green||0.2||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#ff8c26"|&nbsp;||tv_orange||1.0||0.55||0.15||<br />
|- align="center"<br />
|bgcolor="#ff3333"|&nbsp;||tv_red||1.0||0.2||0.2||<br />
|- align="center"<br />
|bgcolor="#ffff33"|&nbsp;||tv_yellow||1.0||1.0||0.2||<br />
|- align="center"<br />
|bgcolor="#ff7fff"|&nbsp;||violet||1.0||0.5||1.0||<br />
|- align="center"<br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple||0.55||0.25||0.60||<br />
|- align="center"<br />
|bgcolor="#d8337f"|&nbsp;||warmpink||0.85||0.20||0.50||<br />
|- align="center"<br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center"<br />
|bgcolor="#ffffff"|&nbsp;||white||1.0||1.0||1.0||<br />
|- align="center"<br />
|bgcolor="#ffff00"|&nbsp;||yellow||1.0||1.0||0.0||<br />
|- align="center"<br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|}<br />
==Chemical element colours==<br />
{| cellpadding="1"<br />
|- align="center"<br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||bgcolor=gray|note<br />
|- align="center"<br />
|bgcolor="#6faafa"|&nbsp;||actinium||0.439215686||0.670588235||0.980392157||<br />
|- align="center"<br />
|bgcolor="#bfa5a5"|&nbsp;||aluminum||0.749019608||0.650980392||0.650980392||<br />
|- align="center"<br />
|bgcolor="#545cf2"|&nbsp;||americium||0.329411765||0.360784314||0.949019608||<br />
|- align="center"<br />
|bgcolor="#9d62b5"|&nbsp;||antimony||0.619607843||0.388235294||0.709803922||<br />
|- align="center"<br />
|bgcolor="#7fd0e2"|&nbsp;||argon||0.501960784||0.819607843||0.890196078||<br />
|- align="center"<br />
|bgcolor="#bd7fe2"|&nbsp;||arsenic||0.741176471||0.501960784||0.890196078||<br />
|- align="center"<br />
|bgcolor="#744f44"|&nbsp;||astatine||0.458823529||0.309803922||0.270588235||<br />
|- align="center"<br />
|bgcolor="#00c800"|&nbsp;||barium||0.000000000||0.788235294||0.000000000||<br />
|- align="center"<br />
|bgcolor="#8a4fe2"|&nbsp;||berkelium||0.541176471||0.309803922||0.890196078||<br />
|- align="center"<br />
|bgcolor="#c2ff00"|&nbsp;||beryllium||0.760784314||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#9d4fb5"|&nbsp;||bismuth||0.619607843||0.309803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#e00037"|&nbsp;||bohrium||0.878431373||0.000000000||0.219607843||<br />
|- align="center"<br />
|bgcolor="#ffb5b5"|&nbsp;||boron||1.000000000||0.709803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#a52929"|&nbsp;||bromine||0.650980392||0.160784314||0.160784314||<br />
|- align="center"<br />
|bgcolor="#ffd88f"|&nbsp;||cadmium||1.000000000||0.850980392||0.560784314||<br />
|- align="center"<br />
|bgcolor="#3cff00"|&nbsp;||calcium||0.239215686||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#a036d3"|&nbsp;||californium||0.631372549||0.211764706||0.831372549||<br />
|- align="center"<br />
|bgcolor="#ffffc7"|&nbsp;||cerium||1.000000000||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#57168f"|&nbsp;||cesium||0.341176471||0.090196078||0.560784314||<br />
|- align="center"<br />
|bgcolor="#1ef01e"|&nbsp;||chlorine||0.121568627||0.941176471||0.121568627||<br />
|- align="center"<br />
|bgcolor="#8a99c7"|&nbsp;||chromium||0.541176471||0.600000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#f08f9f"|&nbsp;||cobalt||0.941176471||0.564705882||0.627450980||<br />
|- align="center"<br />
|bgcolor="#c77f33"|&nbsp;||copper||0.784313725||0.501960784||0.200000000||<br />
|- align="center"<br />
|bgcolor="#775ce2"|&nbsp;||curium||0.470588235||0.360784314||0.890196078||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||deuterium||0.9||0.9||0.9||<br />
|- align="center"<br />
|bgcolor="#d0004f"|&nbsp;||dubnium||0.819607843||0.000000000||0.309803922||<br />
|- align="center"<br />
|bgcolor="#1effc7"|&nbsp;||dysprosium||0.121568627||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b21ed3"|&nbsp;||einsteinium||0.701960784||0.121568627||0.831372549||<br />
|- align="center"<br />
|bgcolor="#00e574"|&nbsp;||erbium||0.000000000||0.901960784||0.458823529||<br />
|- align="center"<br />
|bgcolor="#61ffc7"|&nbsp;||europium||0.380392157||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b21eba"|&nbsp;||fermium||0.701960784||0.121568627||0.729411765||<br />
|- align="center"<br />
|bgcolor="#b2ffff"|&nbsp;||fluorine||0.701960784||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#410066"|&nbsp;||francium||0.258823529||0.000000000||0.400000000||<br />
|- align="center"<br />
|bgcolor="#44ffc7"|&nbsp;||gadolinium||0.270588235||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#c28f8f"|&nbsp;||gallium||0.760784314||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#668f8f"|&nbsp;||germanium||0.400000000||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#ffd023"|&nbsp;||gold||1.000000000||0.819607843||0.137254902||<br />
|- align="center"<br />
|bgcolor="#4cc2ff"|&nbsp;||hafnium||0.301960784||0.760784314||1.000000000||<br />
|- align="center"<br />
|bgcolor="#e5002e"|&nbsp;||hassium||0.901960784||0.000000000||0.180392157||<br />
|- align="center"<br />
|bgcolor="#d8ffff"|&nbsp;||helium||0.850980392||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00ff9c"|&nbsp;||holmium||0.000000000||1.000000000||0.611764706||<br />
|- align="center"<br />
|bgcolor="#a57472"|&nbsp;||indium||0.650980392||0.458823529||0.450980392||<br />
|- align="center"<br />
|bgcolor="#940094"|&nbsp;||iodine||0.580392157||0.000000000||0.580392157||<br />
|- align="center"<br />
|bgcolor="#165487"|&nbsp;||iridium||0.090196078||0.329411765||0.529411765||<br />
|- align="center"<br />
|bgcolor="#e06633"|&nbsp;||iron||0.878431373||0.400000000||0.200000000||<br />
|- align="center"<br />
|bgcolor="#5cb7d0"|&nbsp;||krypton||0.360784314||0.721568627||0.819607843||<br />
|- align="center"<br />
|bgcolor="#6fd3ff"|&nbsp;||lanthanum||0.439215686||0.831372549||1.000000000||<br />
|- align="center"<br />
|bgcolor="#c70066"|&nbsp;||lawrencium||0.780392157||0.000000000||0.400000000||<br />
|- align="center"<br />
|bgcolor="#575961"|&nbsp;||lead||0.341176471||0.349019608||0.380392157||<br />
|- align="center"<br />
|bgcolor="#cc7fff"|&nbsp;||lithium||0.800000000||0.501960784||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00aa24"|&nbsp;||lutetium||0.000000000||0.670588235||0.141176471||<br />
|- align="center"<br />
|bgcolor="#8aff00"|&nbsp;||magnesium||0.541176471||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#9c7ac7"|&nbsp;||manganese||0.611764706||0.478431373||0.780392157||<br />
|- align="center"<br />
|bgcolor="#ea0026"|&nbsp;||meitnerium||0.921568627||0.000000000||0.149019608||<br />
|- align="center"<br />
|bgcolor="#b20ca5"|&nbsp;||mendelevium||0.701960784||0.050980392||0.650980392||<br />
|- align="center"<br />
|bgcolor="#b7b7d0"|&nbsp;||mercury||0.721568627||0.721568627||0.815686275||<br />
|- align="center"<br />
|bgcolor="#54b5b5"|&nbsp;||molybdenum||0.329411765||0.709803922||0.709803922||<br />
|- align="center"<br />
|bgcolor="#c7ffc7"|&nbsp;||neodymium||0.780392157||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#b2e2f5"|&nbsp;||neon||0.701960784||0.890196078||0.960784314||<br />
|- align="center"<br />
|bgcolor="#007fff"|&nbsp;||neptunium||0.000000000||0.501960784||1.000000000||<br />
|- align="center"<br />
|bgcolor="#4fd04f"|&nbsp;||nickel||0.313725490||0.815686275||0.313725490||<br />
|- align="center"<br />
|bgcolor="#72c2c8"|&nbsp;||niobium||0.450980392||0.760784314||0.788235294||<br />
|- align="center"<br />
|bgcolor="#bd0c87"|&nbsp;||nobelium||0.741176471||0.050980392||0.529411765||<br />
|- align="center"<br />
|bgcolor="#266695"|&nbsp;||osmium||0.149019608||0.400000000||0.588235294||<br />
|- align="center"<br />
|bgcolor="#006984"|&nbsp;||palladium||0.000000000||0.411764706||0.521568627||<br />
|- align="center"<br />
|bgcolor="#ff7f00"|&nbsp;||phosphorus||1.000000000||0.501960784||0.000000000||<br />
|- align="center"<br />
|bgcolor="#d0d0e0"|&nbsp;||platinum||0.815686275||0.815686275||0.878431373||<br />
|- align="center"<br />
|bgcolor="#006aff"|&nbsp;||plutonium||0.000000000||0.419607843||1.000000000||<br />
|- align="center"<br />
|bgcolor="#aa5c00"|&nbsp;||polonium||0.670588235||0.360784314||0.000000000||<br />
|- align="center"<br />
|bgcolor="#8f3fd3"|&nbsp;||potassium||0.560784314||0.250980392||0.831372549||<br />
|- align="center"<br />
|bgcolor="#d8ffc7"|&nbsp;||praseodymium||0.850980392||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#a2ffc7"|&nbsp;||promethium||0.639215686||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#00a0ff"|&nbsp;||protactinium||0.000000000||0.631372549||1.000000000||<br />
|- align="center"<br />
|bgcolor="#007c00"|&nbsp;||radium||0.000000000||0.490196078||0.000000000||<br />
|- align="center"<br />
|bgcolor="#418295"|&nbsp;||radon||0.258823529||0.509803922||0.588235294||<br />
|- align="center"<br />
|bgcolor="#267caa"|&nbsp;||rhenium||0.149019608||0.490196078||0.670588235||<br />
|- align="center"<br />
|bgcolor="#097c8c"|&nbsp;||rhodium||0.039215686||0.490196078||0.549019608||<br />
|- align="center"<br />
|bgcolor="#6f2eaf"|&nbsp;||rubidium||0.439215686||0.180392157||0.690196078||<br />
|- align="center"<br />
|bgcolor="#248f8f"|&nbsp;||ruthenium||0.141176471||0.560784314||0.560784314||<br />
|- align="center"<br />
|bgcolor="#cc0059"|&nbsp;||rutherfordium||0.800000000||0.000000000||0.349019608||<br />
|- align="center"<br />
|bgcolor="#8fffc7"|&nbsp;||samarium||0.560784314||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#e5e5e5"|&nbsp;||scandium||0.901960784||0.901960784||0.901960784||<br />
|- align="center"<br />
|bgcolor="#d80044"|&nbsp;||seaborgium||0.850980392||0.000000000||0.270588235||<br />
|- align="center"<br />
|bgcolor="#ffa000"|&nbsp;||selenium||1.000000000||0.631372549||0.000000000||<br />
|- align="center"<br />
|bgcolor="#f0c79f"|&nbsp;||silicon||0.941176471||0.784313725||0.627450980||<br />
|- align="center"<br />
|bgcolor="#bfbfbf"|&nbsp;||silver||0.752941176||0.752941176||0.752941176||<br />
|- align="center"<br />
|bgcolor="#aa5cf2"|&nbsp;||sodium||0.670588235||0.360784314||0.949019608||<br />
|- align="center"<br />
|bgcolor="#00ff00"|&nbsp;||strontium||0.000000000||1.000000000||0.000000000||<br />
|- align="center"<br />
|bgcolor="#4ca5ff"|&nbsp;||tantalum||0.301960784||0.650980392||1.000000000||<br />
|- align="center"<br />
|bgcolor="#3a9d9d"|&nbsp;||technetium||0.231372549||0.619607843||0.619607843||<br />
|- align="center"<br />
|bgcolor="#d37a00"|&nbsp;||tellurium||0.831372549||0.478431373||0.000000000||<br />
|- align="center"<br />
|bgcolor="#2fffc7"|&nbsp;||terbium||0.188235294||1.000000000||0.780392157||<br />
|- align="center"<br />
|bgcolor="#a5544c"|&nbsp;||thallium||0.650980392||0.329411765||0.301960784||<br />
|- align="center"<br />
|bgcolor="#00baff"|&nbsp;||thorium||0.000000000||0.729411765||1.000000000||<br />
|- align="center"<br />
|bgcolor="#00d351"|&nbsp;||thulium||0.000000000||0.831372549||0.321568627||<br />
|- align="center"<br />
|bgcolor="#667f7f"|&nbsp;||tin||0.400000000||0.501960784||0.501960784||<br />
|- align="center"<br />
|bgcolor="#bfc2c7"|&nbsp;||titanium||0.749019608||0.760784314||0.780392157||<br />
|- align="center"<br />
|bgcolor="#2194d5"|&nbsp;||tungsten||0.129411765||0.580392157||0.839215686||<br />
|- align="center"<br />
|bgcolor="#008fff"|&nbsp;||uranium||0.000000000||0.560784314||1.000000000||<br />
|- align="center"<br />
|bgcolor="#a5a5aa"|&nbsp;||vanadium||0.650980392||0.650980392||0.670588235||<br />
|- align="center"<br />
|bgcolor="#419daf"|&nbsp;||xenon||0.258823529||0.619607843||0.690196078||<br />
|- align="center"<br />
|bgcolor="#00bf37"|&nbsp;||ytterbium||0.000000000||0.749019608||0.219607843||<br />
|- align="center"<br />
|bgcolor="#94ffff"|&nbsp;||yttrium||0.580392157||1.000000000||1.000000000||<br />
|- align="center"<br />
|bgcolor="#7c7faf"|&nbsp;||zinc||0.490196078||0.501960784||0.690196078||<br />
|- align="center"<br />
|bgcolor="#94e0e0"|&nbsp;||zirconium||0.580392157||0.878431373||0.878431373||<br />
|}<br />
==Interactive menu colours==<br />
Accessible from Colour submenu of objects<br />
===reds===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff0000"|&nbsp;||red||1.0||0.0||0.0||<br />
|- align="center" <br />
|bgcolor="#ff3333"|&nbsp;||tv_red||1.0||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#b24c66"|&nbsp;||raspberry||0.70||0.30||0.40||<br />
|- align="center" <br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon||0.73||0.55||0.52||<br />
|- align="center" <br />
|bgcolor="#ff9999"|&nbsp;||salmon||1.0||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#ff6b6b"|&nbsp;||deepsalmon||1.00||0.42||0.42||<br />
|- align="center" <br />
|bgcolor="#d8337f"|&nbsp;||warmpink||0.85||0.20||0.50||<br />
|- align="center" <br />
|bgcolor="#b12121"|&nbsp;||firebrick||0.698||0.13||0.13||<br />
|- align="center" <br />
|bgcolor="#993333"|&nbsp;||ruby||0.6||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#8d381c"|&nbsp;||chocolate||0.555||0.222||0.111||<br />
|- align="center" <br />
|bgcolor="#a5512b"|&nbsp;||brown||0.65||0.32||0.17||<br />
|}<br />
===greens===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#00ff00"|&nbsp;||green||0.0||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#33ff33"|&nbsp;||tv_green||0.2||1.0||0.2||<br />
|- align="center" <br />
|bgcolor="#7fff00"|&nbsp;||chartreuse||0.5||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#84bf00"|&nbsp;||splitpea||0.52||0.75||0.00||<br />
|- align="center" <br />
|bgcolor="#8cb266"|&nbsp;||smudge||0.55||0.70||0.40||<br />
|- align="center" <br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center" <br />
|bgcolor="#00ff7f"|&nbsp;||limegreen||0.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#7fff7f"|&nbsp;||lime||0.5||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center" <br />
|bgcolor="#339933"|&nbsp;||forest||0.2||0.6||0.2||<br />
|}<br />
===blues===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#0000ff"|&nbsp;||blue||0.0||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#4c4cff"|&nbsp;||tv_blue||0.3||0.3||1.0||<br />
|- align="center" <br />
|bgcolor="#007fff"|&nbsp;||marine||0.0||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#7f7fff"|&nbsp;||slate||0.5||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center" <br />
|bgcolor="#337fcc"|&nbsp;||skyblue||0.20||0.50||0.80||<br />
|- align="center" <br />
|bgcolor="#7f00ff"|&nbsp;||purpleblue||0.5||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue||0.25||0.25||0.65||<br />
|- align="center" <br />
|bgcolor="#191999"|&nbsp;||density||0.1||0.1||0.6||<br />
|}<br />
===yellows===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ffff00"|&nbsp;||yellow||1.0||1.0||0.0||<br />
|- align="center" <br />
|bgcolor="#ffff33"|&nbsp;||tv_yellow||1.0||1.0||0.2||<br />
|- align="center" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|- align="center" <br />
|bgcolor="#bfff3f"|&nbsp;||limon||0.75||1.00||0.25||<br />
|- align="center" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center" <br />
|bgcolor="#b78c4c"|&nbsp;||sand||0.72||0.55||0.30||<br />
|}<br />
===magentas===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff00ff"|&nbsp;||magenta||1.0||0.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta||1.0||0.2||0.8||<br />
|- align="center" <br />
|bgcolor="#ff007f"|&nbsp;||hotpink||1.0||0.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffa5d8"|&nbsp;||pink||1.0||0.65||0.85||<br />
|- align="center" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center" <br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet||0.70||0.50||0.50||<br />
|- align="center" <br />
|bgcolor="#ff7fff"|&nbsp;||violet||1.0||0.5||1.0||<br />
|- align="center" <br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple||0.55||0.25||0.60||<br />
|- align="center" <br />
|bgcolor="#bf00bf"|&nbsp;||purple||0.75||0.00||0.75||<br />
|- align="center" <br />
|bgcolor="#991999"|&nbsp;||deeppurple||0.6||0.1||0.6||<br />
|}<br />
===cyans===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#00ffff"|&nbsp;||cyan||0.0||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#7fffff"|&nbsp;||aquamarine||0.5||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#3fffbf"|&nbsp;||greencyan||0.25||1.00||0.75||<br />
|- align="center" <br />
|bgcolor="#00bfbf"|&nbsp;||teal||0.00||0.75||0.75||<br />
|- align="center" <br />
|bgcolor="#199999"|&nbsp;||deepteal||0.1||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#66b2b2"|&nbsp;||lightteal||0.4||0.7||0.7||<br />
|}<br />
===oranges===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ff7f00"|&nbsp;||orange||1.0||0.5||0.0||<br />
|- align="center" <br />
|bgcolor="#ff8c26"|&nbsp;||tv_orange||1.0||0.55||0.15||<br />
|- align="center" <br />
|bgcolor="#ffb233"|&nbsp;||brightorange||1.0||0.7||0.2||<br />
|- align="center" <br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange||1.0||0.87||0.37||<br />
|- align="center" <br />
|bgcolor="#c4b200"|&nbsp;||olive||0.77||0.70||0.00||<br />
|- align="center" <br />
|bgcolor="#999919"|&nbsp;||deepolive||0.6||0.6||0.1||<br />
|}<br />
===tints===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat||0.99||0.82||0.65||<br />
|- align="center" <br />
|bgcolor="#a5e5a5"|&nbsp;||palegreen||0.65||0.9||0.65||<br />
|- align="center" <br />
|bgcolor="#bfbfff"|&nbsp;||lightblue||0.75||0.75||1.0||<br />
|- align="center" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow||1.0||1.0||0.5||<br />
|- align="center" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink||1.00||0.75||0.87||<br />
|- align="center" <br />
|bgcolor="#ccffff"|&nbsp;||palecyan||0.8||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#ffcc7f"|&nbsp;||lightorange||1.0||0.8||0.5||<br />
|- align="center" <br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite||0.85||0.85||1.00||<br />
|}<br />
===grays===<br />
{| cellpadding="1" <br />
|- align="center" <br />
!width="20"|&nbsp;||bgcolor=gray width="100"|name||bgcolor=red width="50"|R||bgcolor=green width="50"|G||bgcolor=blue width="50"|B||<br />
|- align="center" <br />
|bgcolor="#ffffff"|&nbsp;||white||1.0||1.0||1.0||<br />
|- align="center" <br />
|bgcolor="#e5e5e5"|&nbsp;||grey90||0.9||0.9||0.9||<br />
|- align="center" <br />
|bgcolor="#cccccc"|&nbsp;||grey80||0.8||0.8||0.8||<br />
|- align="center" <br />
|bgcolor="#b2b2b2"|&nbsp;||grey70||0.7||0.7||0.7||<br />
|- align="center" <br />
|bgcolor="#999999"|&nbsp;||grey60||0.6||0.6||0.6||<br />
|- align="center" <br />
|bgcolor="#7f7f7f"|&nbsp;||grey50||0.5||0.5||0.5||<br />
|- align="center" <br />
|bgcolor="#666666"|&nbsp;||grey40||0.4||0.4||0.4||<br />
|- align="center" <br />
|bgcolor="#4c4c4c"|&nbsp;||grey30||0.3||0.3||0.3||<br />
|- align="center" <br />
|bgcolor="#333333"|&nbsp;||grey20||0.2||0.2||0.2||<br />
|- align="center" <br />
|bgcolor="#191919"|&nbsp;||grey10||0.1||0.1||0.1||<br />
|- align="center" <br />
|bgcolor="#000000"|&nbsp;||black||0.0||0.0||0.0||<br />
|}<br />
==Secondary structure colour schemes==<br />
Accessible from 'by ss' section within Colour submenu of object<br />
{| cellpadding="1" <br />
|- align="center" <br />
!bgcolor=gray width="100" colspan="1"|helix||bgcolor=gray width="100" colspan="1"|sheet||bgcolor=gray width="100" colspan="1"|loop<br />
|- align="center" <br />
|bgcolor="#ff0000"|red||bgcolor="#ffff00"|yellow||bgcolor="#00ff00"|green<br />
|- align="center" <br />
|bgcolor="#00ffff"|cyan||bgcolor="#ff00ff"|magenta||bgcolor="#ff9999"|salmon<br />
|}<br />
==Carbon colour schemes==<br />
*Accessible from 'by element' section within Colour submenu of object<br />
*Only carbon colour is affected, other elements are set to their default element colour<br />
*Separated into five sets:<br />
**main set<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|&nbsp;||(carbon not changed)<br />
|- align="left" <br />
|bgcolor="#33ff33"|&nbsp;||carbon<br />
|- align="left" <br />
|bgcolor="#00ffff"|&nbsp;||cyan<br />
|- align="left" <br />
|bgcolor="#ff33cc"|&nbsp;||lightmagenta<br />
|- align="left" <br />
|bgcolor="#ffff00"|&nbsp;||yellow<br />
|- align="left" <br />
|bgcolor="#ff9999"|&nbsp;||salmon<br />
|- align="left" <br />
|bgcolor="#e5e5e5"|&nbsp;||hydrogen<br />
|- align="left" <br />
|bgcolor="#7f7fff"|&nbsp;||slate<br />
|- align="left" <br />
|bgcolor="#ff7f00"|&nbsp;||orange<br />
|}<br />
**set2<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#7fff7f"|&nbsp;||lime<br />
|- align="left" <br />
|bgcolor="#199999"|&nbsp;||deepteal<br />
|- align="left" <br />
|bgcolor="#ff007f"|&nbsp;||hotpink<br />
|- align="left" <br />
|bgcolor="#ffdd5e"|&nbsp;||yelloworange<br />
|- align="left" <br />
|bgcolor="#8c3f99"|&nbsp;||violetpurple<br />
|- align="left" <br />
|bgcolor="#b2b2b2"|&nbsp;||grey70<br />
|- align="left" <br />
|bgcolor="#007fff"|&nbsp;||marine<br />
|- align="left" <br />
|bgcolor="#c4b200"|&nbsp;||olive<br />
|}<br />
**set3<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#8cb266"|&nbsp;||smudge<br />
|- align="left" <br />
|bgcolor="#00bfbf"|&nbsp;||teal<br />
|- align="left" <br />
|bgcolor="#b27f7f"|&nbsp;||dirtyviolet<br />
|- align="left" <br />
|bgcolor="#fcd1a5"|&nbsp;||wheat<br />
|- align="left" <br />
|bgcolor="#ff7f7f"|&nbsp;||deepsalmon<br />
|- align="left" <br />
|bgcolor="#ffbfdd"|&nbsp;||lightpink<br />
|- align="left" <br />
|bgcolor="#7fffff"|&nbsp;||aquamarine<br />
|- align="left" <br />
|bgcolor="#ffff7f"|&nbsp;||paleyellow<br />
|}<br />
**set4<br />
{| cellpadding="1" <br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#00ff7f"|&nbsp;||limegreen<br />
|- align="left" <br />
|bgcolor="#337fcc"|&nbsp;||skyblue<br />
|- align="left" <br />
|bgcolor="#d8337f"|&nbsp;||warmpink<br />
|- align="left" <br />
|bgcolor="#bfff3f"|&nbsp;||limon<br />
|- align="left" <br />
|bgcolor="#ff7fff"|&nbsp;||violet<br />
|- align="left" <br />
|bgcolor="#d8d8ff"|&nbsp;||bluewhite<br />
|- align="left" <br />
|bgcolor="#3fffbf"|&nbsp;||greencyan<br />
|- align="left" <br />
|bgcolor="#b78c4c"|&nbsp;||sand<br />
|}<br />
**set 5<br />
{| cellpadding="1"<br />
|- align="left" <br />
!width="20"|&nbsp;||bgcolor=gray|name<br />
|- align="left" <br />
|bgcolor="#339933"|&nbsp;||forest<br />
|- align="left" <br />
|bgcolor="#66b2b2"|&nbsp;||lightteal<br />
|- align="left" <br />
|bgcolor="#ba8c84"|&nbsp;||darksalmon<br />
|- align="left" <br />
|bgcolor="#84bf00"|&nbsp;||splitpea<br />
|- align="left" <br />
|bgcolor="#b24c66"|&nbsp;||raspberry<br />
|- align="left" <br />
|bgcolor="#7f7f7f"|&nbsp;||grey50<br />
|- align="left" <br />
|bgcolor="#3f3fa5"|&nbsp;||deepblue<br />
|- align="left" <br />
|bgcolor="#a5512b"|&nbsp;||brown<br />
|}</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Depth_cue&diff=5407Depth cue2006-10-19T14:57:40Z<p>Hsteinbe: /* Syntax */</p>
<hr />
<div>== Overview ==<br />
One can adjust the fog that PyMol overlays on objects in the viewer window. This fog helps to assist in emphasizing what is in the foreground and backgound of the image with respect to the camera.<br />
<br />
In mouse mode, 3-Button Viewing:<br />
<br />
Rear clipping plane- hold down the shift key and the right mouse button and drag the mouse to the right, more fog will be added to the background. Drag to the left and more fog will be removed from the background.<br />
<br />
Front clipping plane- hold down the shift key and the right mouse button and drag the mouse toward you. You should see the clipping plane come into view. Adjust the front and rear clipping plane to focus on the area of the molecule you wish to display.<br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set depth_cue, 1 # turn on depth cueing<br />
set depth_cue, 0 # turn off depth cueing<br />
set fog_start, 0.45 #use a number between 0.01 and 0.99 to adjust where the fog will start in the plane of view. Default is 0.45<br />
</source><br />
<br />
==Example==<br />
{| border="0" cellspacing="0" cellpadding="5" align="center"<br />
|[[Image:DepthCue0.png|thumb|frame|depth_cue=0]]<br />
|[[Image:DepthCue1.png|thumb|frame|depth_cue=1]]<br />
|}<br />
== See Also ==<br />
[[Ray_Trace_Fog]], [[Field_Of_View]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Depth_cue&diff=5406Depth cue2006-10-19T14:54:20Z<p>Hsteinbe: /* See Also */</p>
<hr />
<div>== Overview ==<br />
One can adjust the fog that PyMol overlays on objects in the viewer window. This fog helps to assist in emphasizing what is in the foreground and backgound of the image with respect to the camera.<br />
<br />
In mouse mode, 3-Button Viewing:<br />
<br />
Rear clipping plane- hold down the shift key and the right mouse button and drag the mouse to the right, more fog will be added to the background. Drag to the left and more fog will be removed from the background.<br />
<br />
Front clipping plane- hold down the shift key and the right mouse button and drag the mouse toward you. You should see the clipping plane come into view. Adjust the front and rear clipping plane to focus on the area of the molecule you wish to display.<br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set depth_cue, 1 # turn on depth cueing<br />
set depth_cue, 0 # turn off depth cueing<br />
</source><br />
<br />
==Example==<br />
{| border="0" cellspacing="0" cellpadding="5" align="center"<br />
|[[Image:DepthCue0.png|thumb|frame|depth_cue=0]]<br />
|[[Image:DepthCue1.png|thumb|frame|depth_cue=1]]<br />
|}<br />
== See Also ==<br />
[[Ray_Trace_Fog]], [[Field_Of_View]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Depth_cue&diff=5405Depth cue2006-10-19T14:53:55Z<p>Hsteinbe: /* Overview */</p>
<hr />
<div>== Overview ==<br />
One can adjust the fog that PyMol overlays on objects in the viewer window. This fog helps to assist in emphasizing what is in the foreground and backgound of the image with respect to the camera.<br />
<br />
In mouse mode, 3-Button Viewing:<br />
<br />
Rear clipping plane- hold down the shift key and the right mouse button and drag the mouse to the right, more fog will be added to the background. Drag to the left and more fog will be removed from the background.<br />
<br />
Front clipping plane- hold down the shift key and the right mouse button and drag the mouse toward you. You should see the clipping plane come into view. Adjust the front and rear clipping plane to focus on the area of the molecule you wish to display.<br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set depth_cue, 1 # turn on depth cueing<br />
set depth_cue, 0 # turn off depth cueing<br />
</source><br />
<br />
==Example==<br />
{| border="0" cellspacing="0" cellpadding="5" align="center"<br />
|[[Image:DepthCue0.png|thumb|frame|depth_cue=0]]<br />
|[[Image:DepthCue1.png|thumb|frame|depth_cue=1]]<br />
|}<br />
== See Also ==<br />
[[fog]], [[Ray_Trace_Fog]], [[Field_Of_View]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Depth_cue&diff=5404Depth cue2006-10-19T14:47:56Z<p>Hsteinbe: /* Overview */</p>
<hr />
<div>== Overview ==<br />
One can adjust the fog that PyMol overlays on objects in the viewer window. This fog helps to assist in emphasizing what is in the foreground and backgound of the image with respect to the camera.<br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set depth_cue, 1 # turn on depth cueing<br />
set depth_cue, 0 # turn off depth cueing<br />
</source><br />
<br />
==Example==<br />
{| border="0" cellspacing="0" cellpadding="5" align="center"<br />
|[[Image:DepthCue0.png|thumb|frame|depth_cue=0]]<br />
|[[Image:DepthCue1.png|thumb|frame|depth_cue=1]]<br />
|}<br />
== See Also ==<br />
[[fog]], [[Ray_Trace_Fog]], [[Field_Of_View]]</div>Hsteinbehttps://wiki.pymol.org/index.php?title=Sticks&diff=5587Sticks2005-08-02T16:23:53Z<p>Hsteinbe: </p>
<hr />
<div>A simple PyMol representation. Use<br />
<code><br />
show sticks, SELECTION<br />
</code><br />
where SELECTION is a valid selection or previously defined selection name.<br />
<br />
<br />
== Sticks Radius (Sticks Weight)==<br />
To change the radius for sticks, enter the following:<br />
set stick_radius, VALUE<br />
where <br />
0.0<=VALUE<=1.0<br />
<br />
'''1.0''' is 100% or full radius<br />
<br />
'''0.0''' is 0% or invisible -- so use at least 0.1 or greater<br />
<br />
==Sticks Transparency==<br />
To enable transparency for sticks, enter the following:<br />
set stick_transparency, VALUE<br />
where <br />
0.0<=VALUE<=1.0<br />
<br />
'''1.0''' is 100% transparent -- so invisible<br />
<br />
'''0.0''' is 0% transparent -- so opaque<br />
<br />
<br />
Example<br />
set stick_transparency, 0.45<br />
<br />
<br />
[[Image:Sticks_ex.png|thumb|Example Sticks Representation]]<br />
<br />
[[Category:Representations|Sticks]]</div>Hsteinbe