https://wiki.pymol.org/api.php?action=feedcontributions&feedformat=atom&user=RrowlettPyMOL Wiki - User contributions [en]2026-05-25T14:02:09ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3588Display CCP4 Maps2009-10-21T19:51:38Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a 'Fo-Fc map as you wish. CCP4i will create a 2Fo-Fc map by default. <br />
To make a Fo-Fc map, set F1=DELFWT and PHIC=PHDELWT in the task window. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .map.ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''. Alternatively, you can<br />
increase the sampling rate in Pymol in step 3 below.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.map.ccp4 (you need the ccp4<br />
extension). An object named ''mymap.map'' will be created by pymol. To increase the<br />
sampling rate of the map (desirable if you did not do this at the time of map<br />
generation) issue the command '''map_double mymap.map, -1'''<br />
<br />
4. Identify a selection about which to display your map, ''e.g.''<br />
<pre><br />
select site, resi 39-50 and resn bct<br />
</pre><br />
<br />
5. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap.map, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap.map'',<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit. Note: the map object will be named in pymol whatever the filename was minus the .ccp4 extension<br />
<br />
6. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey50, map # sets map to 50% gray<br />
set mesh_width, 0.5 # makes meshes thinner for ray-tracing<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 # turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off # turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png # output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
= User Notes =<br />
If the ccp4 maps loaded by PyMOL seem smaller/larger than maps in other programs this might be due to normalization. To stop PyMOL from normalizing a cpp4 map simply unset,<br />
<source lang="python"><br />
unset normalize_ccp4_maps<br />
</source><br />
'''before''' loading your ccp4 map.<br />
<br />
= See Also =<br />
[[normalize_ccp4_maps]]<br />
<br />
[[Category:Image_Manipulation|Display CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3587Display CCP4 Maps2009-10-21T19:51:12Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a 'Fo-Fc map as you wish. CCP4i will create a 2Fo-Fc map by default<br />
To make a Fo-Fc map, set F1=DELFWT and PHIC=PHDELWT in the task window. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .map.ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''. Alternatively, you can<br />
increase the sampling rate in Pymol in step 3 below.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.map.ccp4 (you need the ccp4<br />
extension). An object named ''mymap.map'' will be created by pymol. To increase the<br />
sampling rate of the map (desirable if you did not do this at the time of map<br />
generation) issue the command '''map_double mymap.map, -1'''<br />
<br />
4. Identify a selection about which to display your map, ''e.g.''<br />
<pre><br />
select site, resi 39-50 and resn bct<br />
</pre><br />
<br />
5. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap.map, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap.map'',<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit. Note: the map object will be named in pymol whatever the filename was minus the .ccp4 extension<br />
<br />
6. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey50, map # sets map to 50% gray<br />
set mesh_width, 0.5 # makes meshes thinner for ray-tracing<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 # turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off # turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png # output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
= User Notes =<br />
If the ccp4 maps loaded by PyMOL seem smaller/larger than maps in other programs this might be due to normalization. To stop PyMOL from normalizing a cpp4 map simply unset,<br />
<source lang="python"><br />
unset normalize_ccp4_maps<br />
</source><br />
'''before''' loading your ccp4 map.<br />
<br />
= See Also =<br />
[[normalize_ccp4_maps]]<br />
<br />
[[Category:Image_Manipulation|Display CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3586Display CCP4 Maps2009-09-01T12:26:43Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .map.ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''. Alternatively, you can<br />
increase the sampling rate in Pymol in step 3 below.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.map.ccp4 (you need the ccp4<br />
extension). An object named ''mymap.map'' will be created by pymol. To increase the<br />
sampling rate of the map (desirable if you did not do this at the time of map<br />
generation) issue the command '''map_double mymap.map, -1'''<br />
<br />
4. Identify a selection about which to display your map, ''e.g.''<br />
<pre><br />
select site, resi 39-50 and resn bct<br />
</pre><br />
<br />
5. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap.map, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap.map'',<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit. Note: the map object will be named in pymol whatever the filename was minus the .ccp4 extension<br />
<br />
6. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey50, map # sets map to 50% gray<br />
set mesh_width, 0.5 # makes meshes thinner for ray-tracing<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 # turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off # turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png # output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
= User Notes =<br />
If the ccp4 maps loaded by PyMOL seem smaller/larger than maps in other programs this might be due to normalization. To stop PyMOL from normalizing a cpp4 map simply unset,<br />
<source lang="python"><br />
unset normalize_ccp4_maps<br />
</source><br />
'''before''' loading your ccp4 map.<br />
<br />
= See Also =<br />
[[normalize_ccp4_maps]]<br />
<br />
[[Category:Image_Manipulation|Display CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3583Display CCP4 Maps2009-04-03T13:55:29Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .map.ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.map.ccp4 (you need the ccp4<br />
extension). An object named ''mymap.map'' will be created by pymol.<br />
<br />
4. Identify a selection about which to display your map, ''e.g.''<br />
<pre><br />
select site, resi 39-50 and resn bct<br />
</pre><br />
<br />
5. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap.map, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap.map'',<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit. Note: the map object will be named in pymol whatever the filename was minus the .ccp4 extension<br />
<br />
6. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off #turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Image_Manipulation|Display CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3582Display CCP4 Maps2008-04-16T19:34:06Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .map.ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.map.ccp4 (you need the ccp4<br />
extension). An object named ''mymap.map'' will be created by pymol.<br />
<br />
4. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap.map, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap.map,''<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off #turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Image_Manipulation|Display CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3581Display CCP4 Maps2008-02-07T17:00:54Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named ''mymap'' will be created by pymol.<br />
<br />
4. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap,''<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off #turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Image_Manipulation|Display CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3580Display CCP4 Maps2008-02-07T17:00:29Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named ''mymap'' will be created by pymol.<br />
<br />
4. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap,''<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off #turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Image_Manipulation|Display_CCP4_Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3579Display CCP4 Maps2008-02-07T16:59:51Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named ''mymap'' will be created by pymol.<br />
<br />
4. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap,''<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off #turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Image_Manipulation|Publication Quality Images]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3578Display CCP4 Maps2008-02-07T16:58:17Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named ''mymap'' will be created by pymol.<br />
<br />
4. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap,''<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off #turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Image_Manipulation|Publication Quality Images]]<br />
[[Category:Publication_Quality|Publication Quality Images]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8923Sphere quality2007-07-06T15:36:58Z<p>Rrowlett: </p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering. Values >1 may result in poor performance during real-time rotation or translation.<br />
<br />
'''Note''': Selecting values larger than 2 with '''stick_ball''' = 1 (enabled) causes PyMol to crash in the Windows version.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1 (default)<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery><br />
<br />
[[Category:Settings]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3577Display CCP4 Maps2007-07-05T14:01:07Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named ''mymap'' will be created by pymol.<br />
<br />
4. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap,''<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog--optional<br />
set depth_cue, 0 # turns off depth cueing--optional<br />
set ray_shadows, off #turns off ray-tracing shadows<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Advanced_Issues|CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3576Display CCP4 Maps2007-07-05T13:52:48Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under ''Infrequently Used Options''.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named ''mymap'' will be created by pymol.<br />
<br />
4. To display the map around your selection (''e.g.'', named ''site'') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object ''mymap,''<br />
contoured at 2.0 sigma, around the selection ''site'', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cueing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Advanced_Issues|CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8922Sphere quality2007-07-05T13:44:10Z<p>Rrowlett: </p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering. Values >1 may result in poor performance during real-time rotation or translation.<br />
<br />
'''Note''': Selecting values larger than 2 with '''stick_ball''' = 1 (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1 (default)<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery><br />
<br />
[[Category:Settings]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3575Display CCP4 Maps2007-07-05T00:47:36Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Advanced_Issues|CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3574Display CCP4 Maps2007-07-05T00:45:35Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Modeling_and_Editing_Structures|CCP4 Maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3573Display CCP4 Maps2007-07-05T00:43:24Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3572Display CCP4 Maps2007-07-05T00:41:04Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Advanced_Issues|CCP4 maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3571Display CCP4 Maps2007-07-05T00:39:45Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Advanced Issues|CCP4 maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3570Display CCP4 Maps2007-07-05T00:38:08Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Advanced_Issues|CCP4 maps]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3569Display CCP4 Maps2007-07-05T00:36:36Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]<br />
<br />
[[Category:Advanced_Issues|Advanced Issues]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3568Display CCP4 Maps2007-07-05T00:34:53Z<p>Rrowlett: </p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Display_CCP4_Maps&diff=3567Display CCP4 Maps2007-07-05T00:34:08Z<p>Rrowlett: New page: The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images. 1. Use '''fft''' to create a map in CCP4. (This task...</p>
<hr />
<div>The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.<br />
<br />
1. Use '''fft''' to create a map in CCP4. (This task can be run from the ''Run<br />
FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a<br />
simple map or a ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all<br />
atoms in PDB file'. For pymol to read the map later, you will need to<br />
add the file extension .ccp4 to the generated map. You may find this map<br />
too coarse to make for a pretty diagram. You can generate a nicer<br />
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.<br />
I usually take the default values generated by FFT and double them. You<br />
can change grid spacing under 'Infrequently Used Options'.<br />
<br />
2. Open pymol and read in your PDB file. Create a selection about<br />
whatever you want to see the map around. Typically one would display the selection<br />
as sticks.<br />
<br />
3. Open your map in pymol, ''e.g.'' mymap.ccp4 (you need the ccp4<br />
extension). An object named mymap will be created by pymol<br />
<br />
4. To display the map around your selection (''e.g.'', named 'site') issue a<br />
command similar to this:<br />
<pre><br />
isomesh map, mymap, 2.0, site, carve=1.6<br />
</pre><br />
This command will create a mesh map object named ''map'' from the object mymap,<br />
contoured at 2.0 sigma, around the selection 'site', within 1.6A of selected atoms. You can<br />
change the contour level and carve parameter to suit.<br />
<br />
5. For a publication quality figure the following are suggestions:<br />
<source lang="python"><br />
color grey30, map # sets map to 30% gray<br />
bg_color white #sets background to white<br />
set ray_trace_fog, 0 #turns off raytrace fog<br />
set depth_cue, 0 # turns off depth cuing<br />
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image<br />
png image.png #output final image<br />
</source><br />
<br />
You should be able to create an image similar to the following one:<br />
<br />
[[Image:ccp4_map.png|center]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=File:Ccp4_map.png&diff=1681File:Ccp4 map.png2007-07-05T00:33:40Z<p>Rrowlett: CCP4 map rendered in pymol. Labels added in GIMP</p>
<hr />
<div>CCP4 map rendered in pymol. Labels added in GIMP</div>Rrowletthttps://wiki.pymol.org/index.php?title=Linux_Install&diff=12419Linux Install2007-07-04T23:42:07Z<p>Rrowlett: /* xorg.conf for stereo in Fedora Core 6 */</p>
<hr />
<div>Installing PyMol is quite straightforward.<br />
<br />
=PyMol=<br />
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:<br />
* [http://www.python.org/ Python] (with distutils)<br />
* [http://pmw.sf.net Pmw] (Python Megawidgets)<br />
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])<br />
<br />
== Generic Linux ==<br />
<br />
=== 0.99rc1 note! ===<br />
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.<br />
<br />
Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.<br />
<br />
=== From Source ===<br />
* untar the compressed package;<br />
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').<br />
* execute <source lang="python">python setup.py install # you may need to be root</source><br />
* execute <source lang="python">python setup2.py install # you may need to be root</source><br />
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
or for the latest version, <br />
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
The executable name is "pymol.com".<br />
<br />
=== From Package ===<br />
Download the appropriate RPM and use 'rpm' to install it. Typically,<br />
rpm -Uvh rpmFileName.rpm<br />
<br />
===Compiling By Hand===<br />
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. <br />
<br />
Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.<br />
<br />
Here's the basic steps to install by source:<br />
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]<br />
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory<br />
# cd pymol<br />
# cd ext<br />
# vi build.com # edit the build file<br />
# cd ..<br />
# cp setup/Rules.make . # or correct Rules.make file for your machine<br />
# vi Rules.make # make appropriate changes<br />
# vi setup.py # make appropriate changes<br />
# make<br />
<br />
Warnings:<br />
* if you're using a 64-bit machine, lib becomes lib64 for almost everything<br />
* ensure you have the correct Python path and version (is it 2.3? 2.4?)<br />
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])<br />
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)<br />
<br />
Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.<br />
<br />
== Fedora Core Linux (x86) ==<br />
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]<br />
<br />
Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:<br />
<br />
[xray]<br />
name=MOKs RPM Repository fedora $releasever - $basearch - xray<br />
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray<br />
<br />
<br />
you may also need to add the pgp key for the repository before yum will get packages from it by either saying:<br />
<br />
rpm --import http://www.bioxray.dk/~mok/404825e7.asc<br />
<br />
or with older versions of rpm:<br />
<br />
wget http://www.bioxray.dk/~mok/404825e7.asc<br />
rpm --import 404825e7.asc<br />
<br />
<br />
And then issuing the following command as root:<br />
<br />
yum install pymol<br />
<br />
== Gentoo Linux (x86) ==<br />
as root:<br />
emerge pymol<br />
be sure to have the proper OpenGL configuration. For example:<br />
opengl-update ati<br />
opengl-update nvidia<br />
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]<br />
<br />
== SuSe ==<br />
=== 32-bit (x86) ===<br />
See [[#Generic Linux]] above.<br />
<br />
=== 64-bit (x86_64) ===<br />
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).<br />
<br />
To install PyMol<br />
*Ensure your system has it's distutils in place and ready to use. Try the following check:<br />
<source lang="python"><br />
from distutils import *<br />
</source><br />
*Download the [http://pymol.org/ source]<br />
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].<br />
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:<br />
<source lang="python"><br />
import * from Pmw<br />
</source><br />
If errors erupt, investigate.<br />
* decompress the source and cd into the PyMol directory that was just decompressed.<br />
* If upgrading see [[:Category: Upgrading PyMol|below]].<br />
* Now enter the following...<br />
<code><br />
python setup.py build<br><br />
sudo python setup.py install<br><br />
sudo python setup2.py<br />
</code><br />
* The sudo commands will need a root password or someone with sudo capabilities.<br />
<br />
I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:<br />
<source lang="python"><br />
sudo cp ./pymol.com /usr/local/bin<br />
</source><br />
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use<br />
<source lang="python"><br />
sudo cp ./pymol /usr/local/bin<br />
</source><br />
<br />
<br />
You should now have a working PyMol install. <br />
<br />
'''pymol.com''' should now run your new PyMol install.<br />
<br />
==Ubuntu Linux (x86 32,64; mac ppc)==<br />
<br />
http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png<br />
<br />
The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command<br />
<br />
sudo apt-get install pymol<br />
<br />
once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated. <br />
<br />
[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.<br />
<br />
=Preparing your System=<br />
See [[Linux_XFree86_Configuration]].<br />
<br />
==Graphics==<br />
===XFree86 Config===<br />
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.<br />
<br />
[[Category:Installation|Linux Installation]]<br />
<br />
===Xorg===<br />
Adding a <br />
Stereo 3<br />
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf): <br />
<br />
ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync<br />
<br />
appears to slightly improve the stereo quality, in particular when one<br />
displays labels and/or dashes/dots.<br />
<br />
For those having possible driver issues, this link might help<br />
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]<br />
<br />
===xorg.conf for stereo in Fedora Core 6===<br />
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:<br />
<br />
<pre><br />
Driver "nvidia"<br />
</pre><br />
<br />
Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.<br />
<br />
<pre><br />
Section "Extensions"<br />
Option "Composite" "Disable"<br />
EndSection<br />
</pre><br />
<br />
In Section "Screen" add the following line to enable quad-buffered stereo:<br />
<br />
<pre>Option "Stereo" "3"</pre><br />
<br />
=Problems=<br />
<br />
==Input==<br />
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.<br />
<br />
==libnvidia-tls.so.1: cannot handle TLS data==<br />
<br />
If you get an error, upon invoking pymol, of the form<br />
<br />
<pre><br />
Traceback (most recent call last):<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?<br />
import pymol<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?<br />
import _cmd<br />
ImportError: libnvidia-tls.so.1: cannot handle TLS data<br />
</pre><br />
<br />
then try changing the permissons on libnvidia-tls.so.1. i.e,<br />
<br />
<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre></div>Rrowletthttps://wiki.pymol.org/index.php?title=Linux_Install&diff=12418Linux Install2007-07-04T23:41:15Z<p>Rrowlett: /* xorg.conf for stereo in Fedora Core 6 */</p>
<hr />
<div>Installing PyMol is quite straightforward.<br />
<br />
=PyMol=<br />
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:<br />
* [http://www.python.org/ Python] (with distutils)<br />
* [http://pmw.sf.net Pmw] (Python Megawidgets)<br />
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])<br />
<br />
== Generic Linux ==<br />
<br />
=== 0.99rc1 note! ===<br />
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.<br />
<br />
Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.<br />
<br />
=== From Source ===<br />
* untar the compressed package;<br />
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').<br />
* execute <source lang="python">python setup.py install # you may need to be root</source><br />
* execute <source lang="python">python setup2.py install # you may need to be root</source><br />
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
or for the latest version, <br />
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
The executable name is "pymol.com".<br />
<br />
=== From Package ===<br />
Download the appropriate RPM and use 'rpm' to install it. Typically,<br />
rpm -Uvh rpmFileName.rpm<br />
<br />
===Compiling By Hand===<br />
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. <br />
<br />
Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.<br />
<br />
Here's the basic steps to install by source:<br />
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]<br />
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory<br />
# cd pymol<br />
# cd ext<br />
# vi build.com # edit the build file<br />
# cd ..<br />
# cp setup/Rules.make . # or correct Rules.make file for your machine<br />
# vi Rules.make # make appropriate changes<br />
# vi setup.py # make appropriate changes<br />
# make<br />
<br />
Warnings:<br />
* if you're using a 64-bit machine, lib becomes lib64 for almost everything<br />
* ensure you have the correct Python path and version (is it 2.3? 2.4?)<br />
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])<br />
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)<br />
<br />
Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.<br />
<br />
== Fedora Core Linux (x86) ==<br />
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]<br />
<br />
Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:<br />
<br />
[xray]<br />
name=MOKs RPM Repository fedora $releasever - $basearch - xray<br />
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray<br />
<br />
<br />
you may also need to add the pgp key for the repository before yum will get packages from it by either saying:<br />
<br />
rpm --import http://www.bioxray.dk/~mok/404825e7.asc<br />
<br />
or with older versions of rpm:<br />
<br />
wget http://www.bioxray.dk/~mok/404825e7.asc<br />
rpm --import 404825e7.asc<br />
<br />
<br />
And then issuing the following command as root:<br />
<br />
yum install pymol<br />
<br />
== Gentoo Linux (x86) ==<br />
as root:<br />
emerge pymol<br />
be sure to have the proper OpenGL configuration. For example:<br />
opengl-update ati<br />
opengl-update nvidia<br />
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]<br />
<br />
== SuSe ==<br />
=== 32-bit (x86) ===<br />
See [[#Generic Linux]] above.<br />
<br />
=== 64-bit (x86_64) ===<br />
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).<br />
<br />
To install PyMol<br />
*Ensure your system has it's distutils in place and ready to use. Try the following check:<br />
<source lang="python"><br />
from distutils import *<br />
</source><br />
*Download the [http://pymol.org/ source]<br />
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].<br />
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:<br />
<source lang="python"><br />
import * from Pmw<br />
</source><br />
If errors erupt, investigate.<br />
* decompress the source and cd into the PyMol directory that was just decompressed.<br />
* If upgrading see [[:Category: Upgrading PyMol|below]].<br />
* Now enter the following...<br />
<code><br />
python setup.py build<br><br />
sudo python setup.py install<br><br />
sudo python setup2.py<br />
</code><br />
* The sudo commands will need a root password or someone with sudo capabilities.<br />
<br />
I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:<br />
<source lang="python"><br />
sudo cp ./pymol.com /usr/local/bin<br />
</source><br />
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use<br />
<source lang="python"><br />
sudo cp ./pymol /usr/local/bin<br />
</source><br />
<br />
<br />
You should now have a working PyMol install. <br />
<br />
'''pymol.com''' should now run your new PyMol install.<br />
<br />
==Ubuntu Linux (x86 32,64; mac ppc)==<br />
<br />
http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png<br />
<br />
The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command<br />
<br />
sudo apt-get install pymol<br />
<br />
once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated. <br />
<br />
[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.<br />
<br />
=Preparing your System=<br />
See [[Linux_XFree86_Configuration]].<br />
<br />
==Graphics==<br />
===XFree86 Config===<br />
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.<br />
<br />
[[Category:Installation|Linux Installation]]<br />
<br />
===Xorg===<br />
Adding a <br />
Stereo 3<br />
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf): <br />
<br />
ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync<br />
<br />
appears to slightly improve the stereo quality, in particular when one<br />
displays labels and/or dashes/dots.<br />
<br />
For those having possible driver issues, this link might help<br />
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]<br />
<br />
===xorg.conf for stereo in Fedora Core 6===<br />
It is assumed that you have installed the proprietary [http://www.nvidia.com/content/drivers/drivers.asp Nvidia graphics drivers], and that the "Device" section of xorg.conf has the following line in it:<br />
<br />
<pre><br />
Driver "nvidia"<br />
</pre><br />
<br />
Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.<br />
<br />
<pre><br />
Section "Extensions"<br />
Option "Composite" "Disable"<br />
EndSection<br />
</pre><br />
<br />
In Section "Screen" add the following line to enable quad-buffered stereo:<br />
<br />
<pre>Option "Stereo" "3"</pre><br />
<br />
=Problems=<br />
<br />
==Input==<br />
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.<br />
<br />
==libnvidia-tls.so.1: cannot handle TLS data==<br />
<br />
If you get an error, upon invoking pymol, of the form<br />
<br />
<pre><br />
Traceback (most recent call last):<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?<br />
import pymol<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?<br />
import _cmd<br />
ImportError: libnvidia-tls.so.1: cannot handle TLS data<br />
</pre><br />
<br />
then try changing the permissons on libnvidia-tls.so.1. i.e,<br />
<br />
<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre></div>Rrowletthttps://wiki.pymol.org/index.php?title=Linux_Install&diff=12417Linux Install2007-07-04T23:13:56Z<p>Rrowlett: /* xorg.conf for stereo in Fedora Core 6 */</p>
<hr />
<div>Installing PyMol is quite straightforward.<br />
<br />
=PyMol=<br />
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:<br />
* [http://www.python.org/ Python] (with distutils)<br />
* [http://pmw.sf.net Pmw] (Python Megawidgets)<br />
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])<br />
<br />
== Generic Linux ==<br />
<br />
=== 0.99rc1 note! ===<br />
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.<br />
<br />
Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.<br />
<br />
=== From Source ===<br />
* untar the compressed package;<br />
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').<br />
* execute <source lang="python">python setup.py install # you may need to be root</source><br />
* execute <source lang="python">python setup2.py install # you may need to be root</source><br />
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
or for the latest version, <br />
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
The executable name is "pymol.com".<br />
<br />
=== From Package ===<br />
Download the appropriate RPM and use 'rpm' to install it. Typically,<br />
rpm -Uvh rpmFileName.rpm<br />
<br />
===Compiling By Hand===<br />
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. <br />
<br />
Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.<br />
<br />
Here's the basic steps to install by source:<br />
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]<br />
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory<br />
# cd pymol<br />
# cd ext<br />
# vi build.com # edit the build file<br />
# cd ..<br />
# cp setup/Rules.make . # or correct Rules.make file for your machine<br />
# vi Rules.make # make appropriate changes<br />
# vi setup.py # make appropriate changes<br />
# make<br />
<br />
Warnings:<br />
* if you're using a 64-bit machine, lib becomes lib64 for almost everything<br />
* ensure you have the correct Python path and version (is it 2.3? 2.4?)<br />
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])<br />
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)<br />
<br />
Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.<br />
<br />
== Fedora Core Linux (x86) ==<br />
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]<br />
<br />
Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:<br />
<br />
[xray]<br />
name=MOKs RPM Repository fedora $releasever - $basearch - xray<br />
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray<br />
<br />
<br />
you may also need to add the pgp key for the repository before yum will get packages from it by either saying:<br />
<br />
rpm --import http://www.bioxray.dk/~mok/404825e7.asc<br />
<br />
or with older versions of rpm:<br />
<br />
wget http://www.bioxray.dk/~mok/404825e7.asc<br />
rpm --import 404825e7.asc<br />
<br />
<br />
And then issuing the following command as root:<br />
<br />
yum install pymol<br />
<br />
== Gentoo Linux (x86) ==<br />
as root:<br />
emerge pymol<br />
be sure to have the proper OpenGL configuration. For example:<br />
opengl-update ati<br />
opengl-update nvidia<br />
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]<br />
<br />
== SuSe ==<br />
=== 32-bit (x86) ===<br />
See [[#Generic Linux]] above.<br />
<br />
=== 64-bit (x86_64) ===<br />
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).<br />
<br />
To install PyMol<br />
*Ensure your system has it's distutils in place and ready to use. Try the following check:<br />
<source lang="python"><br />
from distutils import *<br />
</source><br />
*Download the [http://pymol.org/ source]<br />
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].<br />
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:<br />
<source lang="python"><br />
import * from Pmw<br />
</source><br />
If errors erupt, investigate.<br />
* decompress the source and cd into the PyMol directory that was just decompressed.<br />
* If upgrading see [[:Category: Upgrading PyMol|below]].<br />
* Now enter the following...<br />
<code><br />
python setup.py build<br><br />
sudo python setup.py install<br><br />
sudo python setup2.py<br />
</code><br />
* The sudo commands will need a root password or someone with sudo capabilities.<br />
<br />
I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:<br />
<source lang="python"><br />
sudo cp ./pymol.com /usr/local/bin<br />
</source><br />
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use<br />
<source lang="python"><br />
sudo cp ./pymol /usr/local/bin<br />
</source><br />
<br />
<br />
You should now have a working PyMol install. <br />
<br />
'''pymol.com''' should now run your new PyMol install.<br />
<br />
==Ubuntu Linux (x86 32,64; mac ppc)==<br />
<br />
http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png<br />
<br />
The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command<br />
<br />
sudo apt-get install pymol<br />
<br />
once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated. <br />
<br />
[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.<br />
<br />
=Preparing your System=<br />
See [[Linux_XFree86_Configuration]].<br />
<br />
==Graphics==<br />
===XFree86 Config===<br />
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.<br />
<br />
[[Category:Installation|Linux Installation]]<br />
<br />
===Xorg===<br />
Adding a <br />
Stereo 3<br />
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf): <br />
<br />
ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync<br />
<br />
appears to slightly improve the stereo quality, in particular when one<br />
displays labels and/or dashes/dots.<br />
<br />
For those having possible driver issues, this link might help<br />
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]<br />
<br />
===xorg.conf for stereo in Fedora Core 6===<br />
It is assumed that you have installed the proprietary Nvidia graphics drivers, and that the "Device" section of xorg.conf has the following line in it:<br />
<br />
<pre><br />
Driver "nvidia"<br />
</pre><br />
<br />
Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.<br />
<br />
<pre><br />
Section "Extensions"<br />
Option "Composite" "Disable"<br />
EndSection<br />
</pre><br />
<br />
In Section "Screen" add the following line to enable quad-buffered stereo:<br />
<br />
<pre>Option "Stereo" "3"</pre><br />
<br />
=Problems=<br />
<br />
==Input==<br />
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.<br />
<br />
==libnvidia-tls.so.1: cannot handle TLS data==<br />
<br />
If you get an error, upon invoking pymol, of the form<br />
<br />
<pre><br />
Traceback (most recent call last):<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?<br />
import pymol<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?<br />
import _cmd<br />
ImportError: libnvidia-tls.so.1: cannot handle TLS data<br />
</pre><br />
<br />
then try changing the permissons on libnvidia-tls.so.1. i.e,<br />
<br />
<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre></div>Rrowletthttps://wiki.pymol.org/index.php?title=Linux_Install&diff=12416Linux Install2007-07-04T23:12:28Z<p>Rrowlett: /* xorg.conf for stereo in Fedora Core 6 */</p>
<hr />
<div>Installing PyMol is quite straightforward.<br />
<br />
=PyMol=<br />
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:<br />
* [http://www.python.org/ Python] (with distutils)<br />
* [http://pmw.sf.net Pmw] (Python Megawidgets)<br />
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])<br />
<br />
== Generic Linux ==<br />
<br />
=== 0.99rc1 note! ===<br />
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.<br />
<br />
Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.<br />
<br />
=== From Source ===<br />
* untar the compressed package;<br />
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').<br />
* execute <source lang="python">python setup.py install # you may need to be root</source><br />
* execute <source lang="python">python setup2.py install # you may need to be root</source><br />
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
or for the latest version, <br />
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
The executable name is "pymol.com".<br />
<br />
=== From Package ===<br />
Download the appropriate RPM and use 'rpm' to install it. Typically,<br />
rpm -Uvh rpmFileName.rpm<br />
<br />
===Compiling By Hand===<br />
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. <br />
<br />
Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.<br />
<br />
Here's the basic steps to install by source:<br />
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]<br />
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory<br />
# cd pymol<br />
# cd ext<br />
# vi build.com # edit the build file<br />
# cd ..<br />
# cp setup/Rules.make . # or correct Rules.make file for your machine<br />
# vi Rules.make # make appropriate changes<br />
# vi setup.py # make appropriate changes<br />
# make<br />
<br />
Warnings:<br />
* if you're using a 64-bit machine, lib becomes lib64 for almost everything<br />
* ensure you have the correct Python path and version (is it 2.3? 2.4?)<br />
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])<br />
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)<br />
<br />
Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.<br />
<br />
== Fedora Core Linux (x86) ==<br />
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]<br />
<br />
Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:<br />
<br />
[xray]<br />
name=MOKs RPM Repository fedora $releasever - $basearch - xray<br />
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray<br />
<br />
<br />
you may also need to add the pgp key for the repository before yum will get packages from it by either saying:<br />
<br />
rpm --import http://www.bioxray.dk/~mok/404825e7.asc<br />
<br />
or with older versions of rpm:<br />
<br />
wget http://www.bioxray.dk/~mok/404825e7.asc<br />
rpm --import 404825e7.asc<br />
<br />
<br />
And then issuing the following command as root:<br />
<br />
yum install pymol<br />
<br />
== Gentoo Linux (x86) ==<br />
as root:<br />
emerge pymol<br />
be sure to have the proper OpenGL configuration. For example:<br />
opengl-update ati<br />
opengl-update nvidia<br />
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]<br />
<br />
== SuSe ==<br />
=== 32-bit (x86) ===<br />
See [[#Generic Linux]] above.<br />
<br />
=== 64-bit (x86_64) ===<br />
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).<br />
<br />
To install PyMol<br />
*Ensure your system has it's distutils in place and ready to use. Try the following check:<br />
<source lang="python"><br />
from distutils import *<br />
</source><br />
*Download the [http://pymol.org/ source]<br />
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].<br />
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:<br />
<source lang="python"><br />
import * from Pmw<br />
</source><br />
If errors erupt, investigate.<br />
* decompress the source and cd into the PyMol directory that was just decompressed.<br />
* If upgrading see [[:Category: Upgrading PyMol|below]].<br />
* Now enter the following...<br />
<code><br />
python setup.py build<br><br />
sudo python setup.py install<br><br />
sudo python setup2.py<br />
</code><br />
* The sudo commands will need a root password or someone with sudo capabilities.<br />
<br />
I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:<br />
<source lang="python"><br />
sudo cp ./pymol.com /usr/local/bin<br />
</source><br />
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use<br />
<source lang="python"><br />
sudo cp ./pymol /usr/local/bin<br />
</source><br />
<br />
<br />
You should now have a working PyMol install. <br />
<br />
'''pymol.com''' should now run your new PyMol install.<br />
<br />
==Ubuntu Linux (x86 32,64; mac ppc)==<br />
<br />
http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png<br />
<br />
The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command<br />
<br />
sudo apt-get install pymol<br />
<br />
once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated. <br />
<br />
[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.<br />
<br />
=Preparing your System=<br />
See [[Linux_XFree86_Configuration]].<br />
<br />
==Graphics==<br />
===XFree86 Config===<br />
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.<br />
<br />
[[Category:Installation|Linux Installation]]<br />
<br />
===Xorg===<br />
Adding a <br />
Stereo 3<br />
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf): <br />
<br />
ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync<br />
<br />
appears to slightly improve the stereo quality, in particular when one<br />
displays labels and/or dashes/dots.<br />
<br />
For those having possible driver issues, this link might help<br />
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]<br />
<br />
===xorg.conf for stereo in Fedora Core 6===<br />
It is assumed that you have installed the proprietary Nvidia graphics drivers, and that the "Device" section of xorg.conf has the following line in it:<br />
<br />
Driver "nvidia"<br />
<br />
Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.<br />
<br />
Section "Extensions"<br />
Option "Composite" "Disable"<br />
EndSection<br />
<br />
In Section "Screen" add the following line to enable quad-buffered stereo:<br />
<br />
Option "Stereo" "3"<br />
<br />
=Problems=<br />
<br />
==Input==<br />
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.<br />
<br />
==libnvidia-tls.so.1: cannot handle TLS data==<br />
<br />
If you get an error, upon invoking pymol, of the form<br />
<br />
<pre><br />
Traceback (most recent call last):<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?<br />
import pymol<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?<br />
import _cmd<br />
ImportError: libnvidia-tls.so.1: cannot handle TLS data<br />
</pre><br />
<br />
then try changing the permissons on libnvidia-tls.so.1. i.e,<br />
<br />
<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre></div>Rrowletthttps://wiki.pymol.org/index.php?title=Linux_Install&diff=12415Linux Install2007-07-04T23:11:57Z<p>Rrowlett: /* Graphics */</p>
<hr />
<div>Installing PyMol is quite straightforward.<br />
<br />
=PyMol=<br />
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:<br />
* [http://www.python.org/ Python] (with distutils)<br />
* [http://pmw.sf.net Pmw] (Python Megawidgets)<br />
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])<br />
<br />
== Generic Linux ==<br />
<br />
=== 0.99rc1 note! ===<br />
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.<br />
<br />
Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.<br />
<br />
=== From Source ===<br />
* untar the compressed package;<br />
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').<br />
* execute <source lang="python">python setup.py install # you may need to be root</source><br />
* execute <source lang="python">python setup2.py install # you may need to be root</source><br />
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
or for the latest version, <br />
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source><br />
The executable name is "pymol.com".<br />
<br />
=== From Package ===<br />
Download the appropriate RPM and use 'rpm' to install it. Typically,<br />
rpm -Uvh rpmFileName.rpm<br />
<br />
===Compiling By Hand===<br />
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand. <br />
<br />
Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.<br />
<br />
Here's the basic steps to install by source:<br />
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]<br />
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory<br />
# cd pymol<br />
# cd ext<br />
# vi build.com # edit the build file<br />
# cd ..<br />
# cp setup/Rules.make . # or correct Rules.make file for your machine<br />
# vi Rules.make # make appropriate changes<br />
# vi setup.py # make appropriate changes<br />
# make<br />
<br />
Warnings:<br />
* if you're using a 64-bit machine, lib becomes lib64 for almost everything<br />
* ensure you have the correct Python path and version (is it 2.3? 2.4?)<br />
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform. For x86_64, besides above files, change following line in contrib/modules/Makefile.pre.in.src pointing to lib64 ([[leafyoung at yahoo dot com]])<br />
LIBP= $(exec_installdir)/lib'''''64'''''/python$(VERSION)<br />
<br />
Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.<br />
<br />
== Fedora Core Linux (x86) ==<br />
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]<br />
<br />
Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:<br />
<br />
[xray]<br />
name=MOKs RPM Repository fedora $releasever - $basearch - xray<br />
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray<br />
<br />
<br />
you may also need to add the pgp key for the repository before yum will get packages from it by either saying:<br />
<br />
rpm --import http://www.bioxray.dk/~mok/404825e7.asc<br />
<br />
or with older versions of rpm:<br />
<br />
wget http://www.bioxray.dk/~mok/404825e7.asc<br />
rpm --import 404825e7.asc<br />
<br />
<br />
And then issuing the following command as root:<br />
<br />
yum install pymol<br />
<br />
== Gentoo Linux (x86) ==<br />
as root:<br />
emerge pymol<br />
be sure to have the proper OpenGL configuration. For example:<br />
opengl-update ati<br />
opengl-update nvidia<br />
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]<br />
<br />
== SuSe ==<br />
=== 32-bit (x86) ===<br />
See [[#Generic Linux]] above.<br />
<br />
=== 64-bit (x86_64) ===<br />
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).<br />
<br />
To install PyMol<br />
*Ensure your system has it's distutils in place and ready to use. Try the following check:<br />
<source lang="python"><br />
from distutils import *<br />
</source><br />
*Download the [http://pymol.org/ source]<br />
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].<br />
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:<br />
<source lang="python"><br />
import * from Pmw<br />
</source><br />
If errors erupt, investigate.<br />
* decompress the source and cd into the PyMol directory that was just decompressed.<br />
* If upgrading see [[:Category: Upgrading PyMol|below]].<br />
* Now enter the following...<br />
<code><br />
python setup.py build<br><br />
sudo python setup.py install<br><br />
sudo python setup2.py<br />
</code><br />
* The sudo commands will need a root password or someone with sudo capabilities.<br />
<br />
I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:<br />
<source lang="python"><br />
sudo cp ./pymol.com /usr/local/bin<br />
</source><br />
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use<br />
<source lang="python"><br />
sudo cp ./pymol /usr/local/bin<br />
</source><br />
<br />
<br />
You should now have a working PyMol install. <br />
<br />
'''pymol.com''' should now run your new PyMol install.<br />
<br />
==Ubuntu Linux (x86 32,64; mac ppc)==<br />
<br />
http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png<br />
<br />
The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command<br />
<br />
sudo apt-get install pymol<br />
<br />
once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated. <br />
<br />
[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.<br />
<br />
=Preparing your System=<br />
See [[Linux_XFree86_Configuration]].<br />
<br />
==Graphics==<br />
===XFree86 Config===<br />
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.<br />
<br />
[[Category:Installation|Linux Installation]]<br />
<br />
===Xorg===<br />
Adding a <br />
Stereo 3<br />
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf): <br />
<br />
ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync<br />
<br />
appears to slightly improve the stereo quality, in particular when one<br />
displays labels and/or dashes/dots.<br />
<br />
For those having possible driver issues, this link might help<br />
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]<br />
<br />
===xorg.conf for stereo in Fedora Core 6===<br />
It is assumed that you have installed the proprietary Nvidia graphics drivers, and that the "Device" section of xorg.conf has the following line in it:<br />
<br />
Driver "nvidia"<br />
<br />
Add the following section to the end of xorg.conf to disable "Composite", which is incompatible with stereographics.<br />
<br />
Section "Extensions"<br />
Option "Composite" "Disable"<br />
EndSection<br />
<br />
In Section "Screen" add the following line to enable quad-buffered stereo:<br />
Option "Stereo" "3"<br />
<br />
=Problems=<br />
<br />
==Input==<br />
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.<br />
<br />
==libnvidia-tls.so.1: cannot handle TLS data==<br />
<br />
If you get an error, upon invoking pymol, of the form<br />
<br />
<pre><br />
Traceback (most recent call last):<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?<br />
import pymol<br />
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?<br />
import _cmd<br />
ImportError: libnvidia-tls.so.1: cannot handle TLS data<br />
</pre><br />
<br />
then try changing the permissons on libnvidia-tls.so.1. i.e,<br />
<br />
<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8921Sphere quality2007-07-04T22:32:09Z<p>Rrowlett: /* Examples */</p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with '''stick_ball''' = 1 (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1 (default)<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery><br />
<br />
[[Category:Settings]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8920Sphere quality2007-07-04T22:31:11Z<p>Rrowlett: </p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with '''stick_ball''' = 1 (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery><br />
<br />
[[Category:Settings]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8919Sphere quality2007-07-04T22:24:29Z<p>Rrowlett: </p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with '''stick_ball''' = on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery><br />
<br />
[[Category:Settings]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Settings&diff=10140Settings2007-07-04T22:08:44Z<p>Rrowlett: </p>
<hr />
<div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 43 done, 475 to go !<br />
<br />
active_selections ray_default_renderer <br />
[[all_states]] ray_direct_shade <br />
[[ambient]] ray_hint_camera <br />
angle_label_position ray_hint_shadow <br />
angle_size ray_improve_shadows <br />
animation ray_interior_color <br />
animation_duration ray_interior_mode <br />
[[antialias]] ray_interior_reflect <br />
async_builds ray_interior_shadows <br />
[[atom_name_wildcard]] ray_interior_texture <br />
auto_classify_atoms ray_legacy_lighting <br />
auto_color ray_max_passes <br />
auto_dss [[ray_opaque_background]] <br />
auto_hide_selections [[ray_orthoscopic]] <br />
auto_indicate_flags ray_oversample_cutoff <br />
auto_number_selections ray_pixel_scale <br />
auto_remove_hydrogens [[ray_shadow]] <br />
auto_sculpt ray_shadow_decay_factor <br />
auto_show_lines ray_shadow_decay_range <br />
auto_show_nonbonded ray_shadow_fudge <br />
auto_show_selections [[ray_shadows]] <br />
auto_show_spheres ray_texture <br />
[[auto_zoom]] ray_texture_settings <br />
[[backface_cull]] ray_trace_depth_factor <br />
batch_prefix ray_trace_disco_factor <br />
[[bg_rgb]] [[ray_trace_fog]] <br />
bonding_vdw_cutoff ray_trace_fog_start <br />
button_mode [[ray_trace_frames]] <br />
button_mode_name ray_trace_gain <br />
cache_display [[Ray#Modes|ray_trace_mode]]<br />
cache_frames ray_trace_slope_factor <br />
cache_memory ray_transparency_contrast <br />
[[cartoon_color]] ray_transparency_shadows <br />
[[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br />
cartoon_debug ray_transparency_specular <br />
[[cartoon_discrete_colors]] ray_triangle_fudge <br />
[[cartoon_dumbbell_length]] [[reflect]] <br />
[[cartoon_dumbbell_radius]] reflect_power <br />
[[cartoon_dumbbell_width]] retain_order <br />
[[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br />
[[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br />
[[cartoon_flat_cycles]] ribbon_power <br />
[[cartoon_flat_sheets]] ribbon_power_b <br />
[[Cartoon_helix_radius]] ribbon_radius <br />
[[cartoon_highlight_color]] [[ribbon_sampling]] <br />
cartoon_ladder_color ribbon_side_chain_helper <br />
cartoon_ladder_mode [[ribbon_smooth]] <br />
cartoon_ladder_radius ribbon_throw <br />
cartoon_loop_cap ribbon_trace_atoms <br />
cartoon_loop_quality [[ribbon_width]] <br />
cartoon_loop_radius robust_logs <br />
[[cartoon_nucleic_acid_color]] rock_delay <br />
[[cartoon_nucleic_acid_mode]] roving_byres <br />
[[cartoon_oval_length]] roving_cartoon <br />
[[cartoon_oval_quality]] roving_delay <br />
[[cartoon_oval_width]] roving_detail <br />
cartoon_power roving_isomesh <br />
cartoon_power_b roving_isosurface <br />
cartoon_putty_quality roving_labels <br />
cartoon_putty_radius roving_lines <br />
cartoon_putty_range roving_map1_level <br />
cartoon_putty_scale_max roving_map1_name <br />
cartoon_putty_scale_min roving_map2_level <br />
cartoon_putty_scale_power roving_map2_name <br />
[[cartoon_rect_length]] roving_map3_level <br />
[[cartoon_rect_width]] roving_map3_name <br />
cartoon_refine roving_nb_spheres <br />
cartoon_refine_normals roving_nonbonded <br />
cartoon_refine_tips roving_origin <br />
cartoon_ring_color roving_origin_z <br />
cartoon_ring_finder roving_origin_z_cushion <br />
[[cartoon_ring_mode]] roving_polar_contacts <br />
cartoon_ring_radius roving_polar_cutoff <br />
[[cartoon_ring_transparency]] roving_ribbon <br />
cartoon_ring_width roving_selection <br />
[[cartoon_round_helices]] roving_spheres <br />
[[cartoon_sampling]] roving_sticks <br />
[[cartoon_side_chain_helper]] scene_animation <br />
cartoon_smooth_cycles scene_animation_duration <br />
cartoon_smooth_first scene_current_name <br />
cartoon_smooth_last scene_loop <br />
[[cartoon_smooth_loops]] scene_restart_movie_delay <br />
cartoon_throw scenes_changed <br />
cartoon_trace_atoms sculpt_angl_weight <br />
[[cartoon_transparency]] sculpt_auto_center <br />
cartoon_tube_cap sculpt_avd_excl <br />
cartoon_tube_quality sculpt_avd_gap <br />
cartoon_tube_radius sculpt_avd_range <br />
[[cavity_cull]] sculpt_avd_weight <br />
cgo_dot_radius sculpt_bond_weight <br />
cgo_dot_width sculpt_field_mask <br />
cgo_line_radius sculpt_hb_overlap <br />
cgo_line_width sculpt_hb_overlap_base <br />
cgo_ray_width_scale sculpt_line_weight <br />
cgo_sphere_quality sculpt_max_max <br />
cgo_transparency sculpt_max_min <br />
clamp_colors sculpt_max_scale <br />
connect_bonded sculpt_max_weight <br />
connect_cutoff sculpt_memory <br />
connect_mode sculpt_min_max <br />
coulomb_cutoff sculpt_min_min <br />
coulomb_dielectric sculpt_min_scale <br />
coulomb_units_factor sculpt_min_weight <br />
cull_spheres sculpt_nb_interval <br />
[[Dash_Gap]] sculpt_plan_weight <br />
[[Dash_Length]] sculpt_pyra_weight <br />
[[Dash_Radius]] sculpt_tors_tolerance <br />
[[Dash_Round_Ends]] sculpt_tors_weight <br />
dash_width sculpt_tri_max <br />
debug_pick sculpt_tri_min <br />
defer_builds_mode sculpt_tri_mode <br />
defer_updates sculpt_tri_scale <br />
[[depth_cue]] sculpt_tri_weight <br />
dihedral_label_position sculpt_vdw_scale <br />
dihedral_size sculpt_vdw_scale14 <br />
direct sculpt_vdw_vis_max <br />
dist_counter sculpt_vdw_vis_mid <br />
distance_exclusion sculpt_vdw_vis_min <br />
dot_color sculpt_vdw_vis_mode <br />
dot_density sculpt_vdw_weight <br />
dot_hydrogens sculpt_vdw_weight14 <br />
dot_lighting sculpting <br />
dot_mode sculpting_cycles <br />
dot_normals secondary_structure <br />
[[dot_radius]] security <br />
dot_solvent sel_counter<br />
[[dot_width]] selection_overlay <br />
draw_frames selection_round_points <br />
editor_auto_dihedral selection_visible_only <br />
editor_auto_origin [[selection_width]] <br />
editor_label_fragments selection_width_max <br />
fast_idle selection_width_scale <br />
fetch_path [[seq_view]] <br />
[[Field_Of_View]] seq_view_alignment <br />
fit_iterations seq_view_color <br />
fit_tolerance seq_view_discrete_by_state <br />
float_labels seq_view_fill_char <br />
[[fog]] seq_view_fill_color <br />
[[fog_start]] seq_view_format <br />
frame seq_view_label_color <br />
full_screen seq_view_label_mode <br />
gamma seq_view_label_spacing <br />
gaussian_b_adjust seq_view_label_start <br />
gaussian_b_floor [[seq_view_location]] <br />
gaussian_resolution seq_view_overlay <br />
gl_ambient seq_view_unaligned_color <br />
h_bond_cone seq_view_unaligned_mode <br />
h_bond_cutoff_center session_file <br />
h_bond_cutoff_edge session_migration <br />
h_bond_exclusion session_version_check <br />
h_bond_max_angle [[shininess]]<br />
h_bond_power_a show_alpha_checker <br />
h_bond_power_b show_progress <br />
[[half_bonds]] simplify_display_lists <br />
hash_max single_image <br />
hide_underscore_names slice_dynamic_grid <br />
idle_delay slice_dynamic_grid_resolution<br />
ignore_case slice_grid <br />
ignore_pdb_segi slice_height_map <br />
image_dots_per_inch slice_height_scale <br />
internal_feedback slice_track_camera <br />
[[Internal Gui|internal_gui]] slow_idle <br />
internal_gui_control_size smooth_color_triangle <br />
internal_gui_mode solvent_radius <br />
internal_gui_width spec_count <br />
[[internal_prompt]] spec_direct <br />
isomesh_auto_state spec_direct_power <br />
[[label_color]] spec_power <br />
[[Label_font_id]] [[spec_reflect]] <br />
[[Label_outline_color]] specular <br />
[[label_position]] specular_intensity <br />
[[label_shadow_mode]] [[sphere_color]] <br />
[[label_size]] sphere_mode <br />
legacy_mouse_zoom sphere_point_max_size <br />
legacy_vdw_radii sphere_point_size <br />
light [[sphere_quality]] <br />
light2 [[sphere_scale]] <br />
light3 sphere_solvent <br />
light4 [[sphere_transparency]] <br />
light5 spheroid_fill <br />
light6 spheroid_scale <br />
light7 spheroid_smooth <br />
light8 ss_helix_phi_exclude <br />
light9 ss_helix_phi_include <br />
[[light_count]] ss_helix_phi_target <br />
line_radius ss_helix_psi_exclude <br />
[[line_smooth]] ss_helix_psi_include <br />
line_stick_helper ss_helix_psi_target <br />
line_width ss_strand_phi_exclude <br />
log_box_selections ss_strand_phi_include <br />
log_conformations ss_strand_phi_target <br />
logging ss_strand_psi_exclude <br />
matrix_mode ss_strand_psi_include <br />
max_threads ss_strand_psi_target <br />
max_triangles state <br />
[[mesh_color]] static_singletons <br />
[[mesh_lighting]] stereo <br />
[[mesh_mode]] stereo_angle <br />
mesh_normals stereo_double_pump_mono <br />
[[mesh_quality]] stereo_mode <br />
mesh_radius stereo_shift <br />
mesh_solvent [[stick_ball]] <br />
[[mesh_type]] [[stick_ball_ratio]] <br />
[[mesh_width]] stick_color <br />
[[min_mesh_spacing]] stick_fixed_radius <br />
mouse_limit [[stick_nub]] <br />
mouse_restart_movie_delay stick_overlap <br />
mouse_scale stick_quality <br />
mouse_selection_mode stick_radius <br />
movie_delay [[stick_transparency]] <br />
movie_loop stick_valence_scale <br />
multiplex stop_on_exceptions <br />
no_idle surface_best <br />
nonbonded_size surface_carve_cutoff <br />
normal_workaround surface_carve_selection <br />
normalize_ccp4_maps surface_carve_state <br />
normalize_grd_maps surface_circumscribe <br />
normalize_o_maps surface_clear_cutoff <br />
nvidia_bugs surface_clear_selection <br />
opaque_background surface_clear_state <br />
[[orthoscopic]] surface_color <br />
overlay surface_debug <br />
overlay_lines surface_miserable <br />
pdb_conect_all surface_mode <br />
pdb_discrete_chains surface_normal <br />
pdb_echo_tags surface_optimize_subsets <br />
pdb_hetatm_sort surface_poor <br />
pdb_honor_model_number surface_proximity <br />
pdb_insertions_go_first surface_quality <br />
pdb_insure_orthogonal surface_ramp_above_mode <br />
pdb_literal_names surface_solvent <br />
pdb_no_end_record surface_trim_cutoff <br />
pdb_reformat_names_mode surface_trim_factor <br />
pdb_retain_ids surface_type <br />
pdb_standard_order suspend_updates <br />
pdb_truncate_residue_name swap_dsn6_bytes <br />
pdb_unbond_cations sweep_angle <br />
pdb_use_ter_records sweep_mode <br />
[[pickable]] sweep_phase <br />
png_file_gamma sweep_speed <br />
png_screen_gamma test1 <br />
power test2 <br />
pqr_no_chain_id text <br />
presentation texture_fonts <br />
presentation_auto_quit [[transparency]] <br />
presentation_auto_start transparency_mode <br />
presentation_mode transparency_picking_mode <br />
preserve_chempy_ids triangle_max_passes <br />
pymol_space_max_blue trim_dots <br />
pymol_space_max_green [[two_sided_lighting]]<br />
pymol_space_max_red use_display_lists <br />
pymol_space_min_factor [[valence]] <br />
raise_exceptions valence_default <br />
rank_assisted_sorts valence_size <br />
ray_blend_blue validate_object_names <br />
ray_blend_colors [[virtual_trackball]] <br />
ray_blend_green wildcard <br />
ray_blend_red wizard_prompt_mode <br />
ray_color_ramps wrap_output <br />
<br />
[[Category:Settings|All Settings]]</div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8918Sphere quality2007-07-04T22:06:52Z<p>Rrowlett: /* Syntax */</p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with '''stick_ball''' = on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8917Sphere quality2007-07-04T22:05:51Z<p>Rrowlett: /* Syntax */</p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with "stick_ball" = on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8916Sphere quality2007-07-04T22:04:41Z<p>Rrowlett: /* Syntax */</p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_quality, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with stick_ball=on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8915Sphere quality2007-07-04T22:04:30Z<p>Rrowlett: /* Syntax */</p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set sphere_qualityl, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with stick_ball=on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8914Sphere quality2007-07-04T22:03:06Z<p>Rrowlett: /* Syntax */</p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set backface_cull, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
<br />
'''Note''': Selecting values larger than 2 with stick_ball=on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8913Sphere quality2007-07-04T22:01:54Z<p>Rrowlett: </p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set backface_cull, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
'''Note''': Selecting values larger than 2 with stick_ball=on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.png|sphere_quality 0<br />
Image:Sphere_quality_1.png|sphere_quality 1<br />
Image:Sphere_quality_2.png|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8912Sphere quality2007-07-04T22:00:50Z<p>Rrowlett: </p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set backface_cull, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
'''Note''': Selecting values larger than 2 with stick_ball=on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:Sphere_quality_0.jpg|sphere_quality 0<br />
Image:Sphere_quality_1.jpg|sphere_quality 1<br />
Image:Sphere_quality_2.jpg|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=File:Sphere_quality_0.png&diff=2825File:Sphere quality 0.png2007-07-04T22:00:10Z<p>Rrowlett: </p>
<hr />
<div>Sample render with sphere_quality=0</div>Rrowletthttps://wiki.pymol.org/index.php?title=File:Sphere_quality_2.png&diff=2703File:Sphere quality 2.png2007-07-04T21:59:28Z<p>Rrowlett: Sample render with sphere_quality=2</p>
<hr />
<div>Sample render with sphere_quality=2</div>Rrowletthttps://wiki.pymol.org/index.php?title=File:Sphere_quality_1.png&diff=2577File:Sphere quality 1.png2007-07-04T21:58:49Z<p>Rrowlett: Sample render with sphere_quality=1 (default value)</p>
<hr />
<div>Sample render with sphere_quality=1 (default value)</div>Rrowletthttps://wiki.pymol.org/index.php?title=File:Sphere_quality_0.png&diff=2824File:Sphere quality 0.png2007-07-04T21:57:59Z<p>Rrowlett: </p>
<hr />
<div></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8911Sphere quality2007-07-04T21:56:45Z<p>Rrowlett: </p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects.<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set backface_cull, <integer><br />
</source><br />
<br />
Larger values of <integer> result in higher quality sphere rendering.<br />
'''Note''': Selecting values larger than 2 with stick_ball=on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
<br />
==Examples==<br />
Open the images to see rendering details.<br />
<gallery><br />
Image:sphere_quality_0.jpg|sphere_quality 0<br />
Image:sphere_quality_1.jpg|sphere_quality 1<br />
Image:sphere_quality_2.jpg|sphere_quality 2<br />
</gallery></div>Rrowletthttps://wiki.pymol.org/index.php?title=Sphere_quality&diff=8910Sphere quality2007-07-04T21:52:19Z<p>Rrowlett: New page: ==Overview== '''sphere_quality''' controls the rendering quality of sphere objects ==Syntax== <source lang="python"> # the default value is 1 set backface_cull, <integer> </source> '''Note''': Select...</p>
<hr />
<div>==Overview==<br />
'''sphere_quality''' controls the rendering quality of sphere objects<br />
<br />
<br />
==Syntax==<br />
<source lang="python"><br />
# the default value is 1<br />
set backface_cull, <integer><br />
</source><br />
<br />
'''Note''': Selecting values larger than 2 with stick_ball=on (enabled) causes PyMol 0.99 to crash in Windows.<br />
<br />
<br />
==Examples==<br />
<gallery><br />
Image:sphere_quality_0.jpg|sphere_quality 0<br />
Image:sphere_quality_1.jpg|sphere_quality 1<br />
Image:sphere_quality_2.jpg|sphere_quality 2<br />
</gallery></div>Rrowlett