https://wiki.pymol.org/api.php?action=feedcontributions&feedformat=atom&user=EsguerraPyMOL Wiki - User contributions [en]2026-05-30T17:07:46ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=3DNA&diff=127523DNA2015-05-08T12:57:27Z<p>Esguerra: /* Overview */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://x3dna.org/] provides a ruby script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA [http://x3dna.org/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<source lang="bash"> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</source><br />
<br />
The pdb_get python script comes from [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]Dr. Robert Campbell's website.<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
set ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
[[http://mesguerra.org/render/render.htm]]<br />
<br />
[[Category:Nucleic_Acids]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=127513DNA2015-05-08T11:01:02Z<p>Esguerra: /* Overview */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://x3dna.org/] provides a ruby script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V2.2 [http://x3dna.org/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<source lang="bash"> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</source><br />
<br />
The pdb_get python script comes from [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]Dr. Robert Campbell's website.<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
set ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
[[http://mesguerra.org/render/render.htm]]<br />
<br />
[[Category:Nucleic_Acids]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=127503DNA2015-05-08T07:05:15Z<p>Esguerra: /* More */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] or 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<source lang="bash"> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</source><br />
<br />
The pdb_get python script comes from [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]Dr. Robert Campbell's website.<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
set ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
[[http://mesguerra.org/render/render.htm]]<br />
<br />
[[Category:Nucleic_Acids]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=Label&diff=7818Label2014-02-18T11:07:26Z<p>Esguerra: </p>
<hr />
<div>[[Image:Pl.png|right|500px]]<br />
<br />
The [[Label]] command controls how PyMOL draws text labels for PyMOL objects.<br />
<br />
= Details =<br />
Labeling is important so there are many options for your fine tuning needs. You can change the [[Label_size|label size]], [[Label_color|label color]], positioning, [[Label_font_id|font]], the [[Label_outline_color|label outline color]] that masks the font and much, much more.<br />
<br />
You can have PyMOL label atoms by properties or arbitrary strings as you want; you can even use Unicode fonts for special symbols like, <math>\alpha, \beta, \pm, \textrm{\AA}</math>, etc.<br />
<br />
The following gallery shows some examples of how extensible the [[Label]] command is. <br />
<gallery heights="180px" widths="200px" align="center" perrow="3"><br />
Image:Label_pre.png|Simple label<br />
Image:New_fonts.jpeg|Example showing usage of Unicode fonts for special characters, see [[label_font_id]].<br />
Image:Font_ex.png|Another example with Unicode fonts<br />
Image:Label_ex.png|Example label<br />
Image:Ls0.png|Label shadows turned off<br />
Image:Ls2.png|Label shadows turned on<br />
</gallery><br />
<br />
==Built-in Object Properties==<br />
Aside from arbitrary string labels, like "This is the catalytic residue" for an atom/residue you can also use the following built-in molecular properties:<br />
* '''name''', the atom name<br />
* '''resn''', the residue name<br />
*'''resi''', the residue number/identifier<br />
*'''chain''', the chain name<br />
*'''q''', charge<br />
*'''b''', the occupancy/b-factor<br />
*'''segi''', the segment identifier<br />
*'''type''' ''(ATOM,HETATM)'', the type of atom<br />
*'''formal_charge''', the formal charge<br />
*'''partial_charge''', the partial charge<br />
*'''numeric_type''', the numeric type<br />
*'''text_type''', the text type<br />
<br />
You can use one of these properties as:<br />
<source lang="python"><br />
# simple example: label residue 22's atoms with their names<br />
label i. 22, name<br />
<br />
# Label residue #44's alpha carbon with it's residue name, residue number and B-factor.<br />
label n. CA and i. 44, "(%s, %s, %s)" % (resn, resi, b)<br />
</source><br />
<br />
See the syntax and examples below for more info.<br />
<br />
=Syntax=<br />
To use the label command follow this syntax:<br />
<source lang="python"><br />
# labeling syntax<br />
label [ selection[, expression]]<br />
</source><br />
where '''selection''' is some object/selection you want to label and '''expression''' is some string (or set of strings) which PyMOL is to use to label the given selection.<br />
<br />
We have plenty of examples. See [[#Examples|the examples]] below.<br />
<br />
=Settings=<br />
Here are all the label settings and their general effect. For each label setting, see the respective web page for more details.<br />
<br />
'''[[label_angle_digits]]'''<br />
:: sets the number of decimals in angle label.<br />
'''[[label_distance_digits]]'''<br />
:: sets the number of decimals in distance label.<br />
'''[[label_shadow_mode]]'''<br />
:: sets whether or not PyMOL will ray trace shadows for your label text. Eg: <source lang="python">set label_shadow_mode, 2</source><br />
'''[[label_color]]'''<br />
:: sets the color of the label text. Note that you can have labels of different colors for different objects or selections. Some examples:<br />
<source lang="python"><br />
# per-object:<br />
set label_color, color-name, object-name #eg, set label-color, magenta, /protein<br />
<br />
# per-atom:<br />
set label_color, color-name, selection #eg, set label-color, marine, /protein/A/A/23/CA<br />
<br />
# another example<br />
fragment arg<br />
label all, name<br />
set label_color, yellow, arg<br />
set label_color, red, elem c<br />
</source><br />
<br />
'''[[label_font_id]]'''<br />
:: sets the font to render your label. There are 12 different fonts from 5&mdash;16. Numbers 15 and 16 are special for unicode. Eg: <source lang="python">set label_font_id, 12</source>. See the [[label_font_id]] page for explicit examples on how to use unicode characters in PyMOL labels.<br />
'''[[label_size]]'''<br />
:: sets the size of the text. You can use positive numbers 2, 3, 4, etc for point sizes, or negative numbers for Angstrom-based sizes. Default is 14 points. Labels in Angstrom-size scale with the distance from the front plane, labels in point-size don't. Eg: <source lang="python">set label_size, -2 #results in a size of 2 Angstroms</source><br />
'''[[label_digits]]'''<br />
:: sets the number of decimals in label. It affects all digits only if label_distance_digits or label_dihedral_digits or label_angle_digits are set to -1.<br />
'''[[label_outline_color]]'''<br />
:: each label is outlined (so you can do white-on-white labels, for example). This options sets the color of the label outline. Eg. <source lang="python">set label_outline_color, orange</source><br />
'''[[label_dihedral_digits]]'''<br />
:: sets the number of decimals in dihedral label.<br />
'''[[label_position]]'''<br />
:: sets any offset from the original X,Y,Z coordinates for the label. If you like to use the mouse, you can enter [[edit_mode]] and '''ctrl-left_click''' to drag labels around; '''ctrl-shift-left_click''' will let you move the labels in the z-direction. '''"Save labels"-workaround''' If you want to save the position of your labels, the best way might be to create a new object and move the atoms in this object. Since the labels are positioned from the atom positions this is an indirect way of moving the labels and being able to save them.<br />
<br />
=Examples=<br />
<source lang="python"><br />
#1.<br />
# make a very simple label on the 14th alpha carbon.<br />
label n. CA and i. 14, "This is carbon 14."<br />
<br />
#2.<br />
# make a fake scene label; use this to label entire scenes, not just atoms/bonds.<br />
pseudoatom foo<br />
label foo, "Once upon a time..."<br />
<br />
#3.<br />
# make a huge label<br />
set label_size, -5<br />
pseudoatom foo<br />
label foo, "This is large text"<br />
<br />
#4. Partial Charge<br />
label (chain A),chain<br />
label (n;ca),"%s-%s" % (resn,resi)<br />
label (resi 200),"%1.3f" % partial_charge<br />
<br />
<br />
#5. The gallery image above Label_ex.png was created with this code<br />
# and finally, some labels were moved around in '''edit_mode'''.<br />
label (resi 200),"%1.3f" % b<br />
set label_font_id, 10<br />
set label_size, 10<br />
<br />
#6. This example shows how to label a selection with the <br />
# XYZ coordinates of the atoms <br />
from pymol import stored<br />
stored.pos = []<br />
# select the carbon atoms in my hetero atoms to label<br />
select nn, het and e. C<br />
# get the XYZ coordinates and put htem into stored.pos<br />
iterate_state 1, (nn), stored.pos.append((x,y,z))<br />
# label all N atoms. You need the pop() function or else<br />
# PyMOL will complain b/c you didn't provide enough coords.<br />
label nn, ("%5.5s, %5.5s, %5.5s") % stored.pos.pop()<br />
</source><br />
<br />
= User Comments =<br />
==Labels Using ID Numbers==<br />
The following commnent,<br />
<source lang="python"><br />
label SELECTION, " %s" % ID <br />
</source><br />
labels the SELECTION with atom ID numbers.<br />
<br />
You can make more complicated selections/lables such as<br />
<source lang="python"><br />
label SELECTION, " %s:%s %s" % (resi, resn, name)<br />
</source><br />
which will give you something like "GLU:139 CG"<br />
<br />
==Labels Using One Letter Abbreviations==<br />
* First, Add this to your $HOME/.pymolrc file:<br />
<source lang="python"><br />
# start $HOME/.pymolrc modification<br />
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \<br />
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', \<br />
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \<br />
'GLY':'G', 'PRO':'P', 'CYS':'C'}<br />
# end modification<br />
</source><br />
<br />
* Second, instead of:<br />
<source lang="python"><br />
label n. ca, resn<br />
</source><br />
use:<br />
<source lang="python"><br />
label n. ca, one_letter[resn]<br />
</source><br />
or: ( to get something like D85)<br />
<source lang="python"><br />
label n. ca, "%s%s" %(one_letter[resn],resi)<br />
</source><br />
<br />
==Labels and defer_builds_mode==<br />
If You have a weak video card, You might want to set<br />
<source lang="python"><br />
set defer_builds_mode, 5<br />
</source><br />
It helps a lot but breaks labels rendering. You can use<br />
<source lang="python"><br />
set defer_builds_mode, 4<br />
</source><br />
instead.<br />
<br />
=See Also=<br />
[[:Category:Labeling]]<br />
<br />
All the settings posted above.<br />
<br />
[[Category:Labeling|Label]]<br />
[[Category:Commands|Label]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=Load_Traj&diff=6814Load Traj2012-06-26T16:02:43Z<p>Esguerra: /* NOTES */</p>
<hr />
<div>'''load_traj''' reads trajectory files (currently just AMBER files). The file extension is used to determine the format. AMBER files must end in ".trj" <br />
<br />
In newer builds of PyMOL (namely, version 1.0 or newer), several additional formats are accepted. CHARMM trajectories (".dcd") are also valid files and only require a structure to be loaded first while the trajectory file gets loaded as sequential states into the associated object. However, it should be noted that, unless the [[defer_builds_mode]] is set (to 3), loading a large trajectory may take up a lot of RAM.<br />
<br />
===USAGE===<br />
<source lang="python"><br />
load_traj filename [,object [,state [,format [,interval [,average ]<br />
[,start [,stop [,max [,selection [,image [,shift <br />
]]]]]]]]]<br />
</source><br />
<br />
===PYMOL API===<br />
<source lang="python"> <br />
cmd.load_traj(filename,object='',state=0,format='',interval=1,<br />
average=1,start=1,stop=-1,max=-1,selection='all',image=1,<br />
shift="[0.0,0.0,0.0]")<br />
</source><br />
<br />
===NOTES===<br />
*You must first load a corresponding topology file before attempting to load a trajectory file.<br />
*PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the [http://amber.scripps.edu/tutorials/basic/tutorial5/index.html ptraj] program first to do this.<br />
*The average option is not a running average. To perform this type of average, use the [[smooth]] command after loading the trajectory file.<br />
*For quickly viewing Trajectories as a movie, use the [[mset]] command to map each state to a movie frame.<br />
<br />
useful notes from the email list:<br />
<br/><br />
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg04272.html<br />
<br/><br />
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10266.html<br />
<br />
in one line convert dcd and psf to pdb :<br />
<br />
catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd<br />
<br />
===SEE ALSO===<br />
[[Load]], [[defer_builds_mode]]<br />
<br />
[[Category:Commands|Load Traj]]<br />
[[Category:Performance|Load Traj]]<br />
[[Category:States|Load Traj]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=Load_Traj&diff=6813Load Traj2012-06-26T16:02:24Z<p>Esguerra: /* NOTES */</p>
<hr />
<div>'''load_traj''' reads trajectory files (currently just AMBER files). The file extension is used to determine the format. AMBER files must end in ".trj" <br />
<br />
In newer builds of PyMOL (namely, version 1.0 or newer), several additional formats are accepted. CHARMM trajectories (".dcd") are also valid files and only require a structure to be loaded first while the trajectory file gets loaded as sequential states into the associated object. However, it should be noted that, unless the [[defer_builds_mode]] is set (to 3), loading a large trajectory may take up a lot of RAM.<br />
<br />
===USAGE===<br />
<source lang="python"><br />
load_traj filename [,object [,state [,format [,interval [,average ]<br />
[,start [,stop [,max [,selection [,image [,shift <br />
]]]]]]]]]<br />
</source><br />
<br />
===PYMOL API===<br />
<source lang="python"> <br />
cmd.load_traj(filename,object='',state=0,format='',interval=1,<br />
average=1,start=1,stop=-1,max=-1,selection='all',image=1,<br />
shift="[0.0,0.0,0.0]")<br />
</source><br />
<br />
===NOTES===<br />
*You must first load a corresponding topology file before attempting to load a trajectory file.<br />
*PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the [http://amber.scripps.edu/tutorials/basic/tutorial5/index.html ptraj] program first to do this.<br />
*The average option is not a running average. To perform this type of average, use the [[smooth]] command after loading the trajectory file.<br />
*For quickly viewing Trajectories as a movie, use the [[mset]] command to map each state to a movie frame.<br />
<br />
useful notes from the email list<br />
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg04272.html<br />
<br/><br />
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10266.html<br />
<br />
in one line convert dcd and psf to pdb :<br />
<br />
catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd<br />
<br />
===SEE ALSO===<br />
[[Load]], [[defer_builds_mode]]<br />
<br />
[[Category:Commands|Load Traj]]<br />
[[Category:Performance|Load Traj]]<br />
[[Category:States|Load Traj]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=Load_Traj&diff=6812Load Traj2012-06-26T16:02:03Z<p>Esguerra: </p>
<hr />
<div>'''load_traj''' reads trajectory files (currently just AMBER files). The file extension is used to determine the format. AMBER files must end in ".trj" <br />
<br />
In newer builds of PyMOL (namely, version 1.0 or newer), several additional formats are accepted. CHARMM trajectories (".dcd") are also valid files and only require a structure to be loaded first while the trajectory file gets loaded as sequential states into the associated object. However, it should be noted that, unless the [[defer_builds_mode]] is set (to 3), loading a large trajectory may take up a lot of RAM.<br />
<br />
===USAGE===<br />
<source lang="python"><br />
load_traj filename [,object [,state [,format [,interval [,average ]<br />
[,start [,stop [,max [,selection [,image [,shift <br />
]]]]]]]]]<br />
</source><br />
<br />
===PYMOL API===<br />
<source lang="python"> <br />
cmd.load_traj(filename,object='',state=0,format='',interval=1,<br />
average=1,start=1,stop=-1,max=-1,selection='all',image=1,<br />
shift="[0.0,0.0,0.0]")<br />
</source><br />
<br />
===NOTES===<br />
*You must first load a corresponding topology file before attempting to load a trajectory file.<br />
*PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the [http://amber.scripps.edu/tutorials/basic/tutorial5/index.html ptraj] program first to do this.<br />
*The average option is not a running average. To perform this type of average, use the [[smooth]] command after loading the trajectory file.<br />
*For quickly viewing Trajectories as a movie, use the [[mset]] command to map each state to a movie frame.<br />
<br />
useful notes from the email list<br />
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg04272.html<br />
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10266.html<br />
<br />
in one line convert dcd and psf to pdb :<br />
<br />
catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd<br />
<br />
===SEE ALSO===<br />
[[Load]], [[defer_builds_mode]]<br />
<br />
[[Category:Commands|Load Traj]]<br />
[[Category:Performance|Load Traj]]<br />
[[Category:States|Load Traj]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=Nucleic_Acid_Sequence&diff=7904Nucleic Acid Sequence2012-05-22T07:02:24Z<p>Esguerra: /* Building a Nucleic Acid Sequence */</p>
<hr />
<div>== Building a Nucleic Acid Sequence ==<br />
At this time there is no known method by which to build nucleic acid sequences in PyMol. <br />
That being said, you can however use third party software to get the job done. <br />
<br />
Check out these programs:<br />
# [http://x3dna.org 3DNA]<br />
# [http://www.scripps.edu/mb/case/Biomer/ B (aka "Biomer")] <br />
# [http://namot.lanl.gov/ NAMOT]<br />
# Enter sequence into web interface and get a pdb file back (Uses NAB - Nucleic Acid Builder): http://structure.usc.edu/make-na/<br />
# Enter sequence into web interface and get a pdb file back (Uses 3DNA): http://w3dna.rutgers.edu/rebuild/fiberch<br />
# Enter sequence into web interface and get a pdb file back (Also uses 3DNA): http://haddock.science.uu.nl/services/3DDART/<br />
<br />
*More info on NAB at: http://casegroup.rutgers.edu/casegr-sh-2.2.html</div>Esguerrahttps://wiki.pymol.org/index.php?title=Git_install_scripts&diff=7547Git install scripts2012-02-17T10:13:37Z<p>Esguerra: moved Git install to Git install scripts: Confusing title with an eventual git install of pymol source.</p>
<hr />
<div>== Manual download of scripts ==<br />
If you don't have the option or want't to install git on your system, then go to<br />
https://github.com/Pymol-Scripts/Pymol-script-repo<br />
Click the "ZIP" button, near the top left corner.<br />
Now unpack the files to a directory. For example:<br />
C:/Users/YOURNAME/Documents/Pymol-script-repo<br />
or<br />
/home/YOURNAME/Software/pymol<br />
<br />
Now go to: '''Adding Pymol-script-repo to PyMOL search path''' [http://www.pymolwiki.org/index.php/Git_install#Adding_Pymol-script-repo_to_PyMOL_search_path]<br />
<br />
== Git install instructions ==<br />
=== For Windows users ===<br />
# Install [http://code.google.com/p/msysgit/downloads/list?can=3&q=official+Git Git for Windows].<br />
Use following settings in options, [http://www.geekgumbo.com/2010/04/09/installing-git-on-windows/ (You can read more here)].<br />
* Windows Explorer Integration -> Context Menu Entries -> Git Bash Here + Git GUI here<br />
* Run Git and included Unix tools from Windows Command prompts<br />
* Checkout Windows style, commit Unix-style endings<br />
<br />
# Navigate to: '''C:\Users\YOURNAME\Documents\pymol'''<br />
# Right click in folder -> Select: Git Gui -> Clone Existing Repository<br />
# Source Location: git://github.com/Pymol-Scripts/Pymol-script-repo.git<br />
# Target Directory: C:\\Users\\YOURNAME\\Documents\\pymol\Pymol-script-repo<br />
#: A backslash "\" in a string is [http://effbot.org/pyref/string-literals.htm is used for escape sequences]. To get a real backslash in a string, use double backslash "\\" <br />
You now have all the scripts available in your directory.<br />
<br />
Add '''python.exe''' to your '''PATH''', so external .py scripts can be executed.<br><br />
Open control panel. Search for, and click: '''Edit environment variables for your account'''<br><br />
Add to end of variable PATH: ''';C:\Python27''' (Or other path to your python python.exe)<br><br />
Click start button, and open '''cmd.exe'''. Try starting python by writing: '''python'''<br />
<br />
=== For Linux users ===<br />
# Install git<br />
# Debian/Ubuntu/Mint<br />
sudo apt-get install git<br />
# Fedora<br />
su -c 'yum install git'<br />
# openSUSE<br />
sudo zypper in git<br />
<br />
# Navigate to desired folder: <br />
cd /home/YOURNAME/Software/pymol<br />
git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git<br />
You now have all the scripts available in: /home/YOURNAME/Software/pymol/Pymol-script-repo<br />
<br />
== Adding Pymol-script-repo to PyMOL search path ==<br />
You now have to add the "Pymol-script-repo" directory to the PyMOL search path. <br />
<br />
The project also have automatically plugin installer: http://www.pymolwiki.org/index.php/plugindirectory <br><br />
This is activated with: '''import plugins'''. <br><br />
'''You have to remove old installations of plugins first, to get the automatic plugin installation to work.'''<br />
=== For Windows users ===<br />
# Open notepad<br />
# Write (Remember double backslashes)<br />
import sys,os<br />
sys.path.append('C:\\Users\\YOURNAME\\Documents\\pymol\\Pymol-script-repo')<br />
os.environ['PYMOL_GIT_MOD']='C:\\Users\\YOURNAME\\Documents\\pymol\\Pymol-script-repo\\modules'<br />
import plugins<br />
os.chdir('C:\\Users\\YOURNAME\\Documents\\pymol') # Your standard working dir<br />
Save under: '''C:\Users\YOURNAME\pymolrc.pym''' (Set: "Save as type" to "All files")<br />
<br />
=== For Linux users ===<br />
gedit ~/.pymolrc<br />
Write<br />
import sys,os<br />
sys.path.append('/home/YOU/Software/pymol/Pymol-script-repo')<br />
os.environ['PYMOL_GIT_MOD']='/home/YOU/Software/pymol/Pymol-script-repo/modules'<br />
import plugins<br />
os.chdir('/home/YOU/Software/pymol/') # Your standard working dir<br />
Save and exit<br />
<br />
== Test the Scripts ==<br />
Now start PyMOL, and test in PyMOL.<br />
print sys.path<br />
import colorbydisplacement<br />
help(colorbydisplacement)<br />
<br />
== Get latest changes to scripts ==<br />
If new scripts are available or changes have been made, then:<br />
=== For windows users ===<br />
# Navigate to '''C:\Users\YOURNAME\Documents\Pymol-script-repo'''<br />
# Right click in folder -> Select: Git Bash<br />
# Write in terminal<br />
git pull origin master<br />
<br />
=== For Ubuntu/Mint users ===<br />
# Navigate to '''/home/YOURNAME/Software/pymol/Pymol-script-repo'''<br />
# Write in terminal.<br />
git pull origin master<br />
<br />
= Do you want to contribute with a script? =<br />
Information how to contribute scripts to the repository. It's easy! <br><br />
http://www.pymolwiki.org/index.php/git_authors</div>Esguerrahttps://wiki.pymol.org/index.php?title=Git_install&diff=6053Git install2012-02-17T10:13:37Z<p>Esguerra: moved Git install to Git install scripts: Confusing title with an eventual git install of pymol source.</p>
<hr />
<div>#REDIRECT [[Git install scripts]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36743DNA2012-02-17T10:04:18Z<p>Esguerra: /* More */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] or 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<source lang="bash"> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</source><br />
<br />
The pdb_get python script comes from [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]Dr. Robert Campbell's website.<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
set ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
[[http://mesguerra.net/render/render.htm]]<br />
<br />
[[Category:Nucleic_Acids]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36733DNA2009-04-14T20:19:47Z<p>Esguerra: /* Invoking */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] or 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<source lang="bash"> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</source><br />
<br />
The pdb_get python script comes from [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]Dr. Robert Campbell's website.<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
set ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]<br />
<br />
[[Category:Nucleic_Acids]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36713DNA2009-02-24T12:09:56Z<p>Esguerra: /* Syntax */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] or 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
set ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]<br />
<br />
[[Category:Nucleic_Acids]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36703DNA2009-02-24T12:05:37Z<p>Esguerra: </p>
<hr />
<div>== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] or 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]<br />
<br />
[[Category:Nucleic_Acids]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36683DNA2008-03-07T20:22:33Z<p>Esguerra: /* More */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
For more examples of figures obtained using 3DNA and pymol follow the next link:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36673DNA2008-03-07T20:21:53Z<p>Esguerra: /* More */</p>
<hr />
<div>== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
More examples of figures obtained using 3DNA and pymol:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36663DNA2008-03-07T20:18:57Z<p>Esguerra: </p>
<hr />
<div><br />
== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=User_talk:Esguerra&diff=10711User talk:Esguerra2008-03-07T20:18:43Z<p>Esguerra: User talk:Esguerra moved to 3DNA</p>
<hr />
<div>#REDIRECT [[3DNA]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36653DNA2008-03-07T20:18:43Z<p>Esguerra: User talk:Esguerra moved to 3DNA</p>
<hr />
<div>= 3DNA =<br />
<br />
== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36643DNA2008-03-07T00:50:21Z<p>Esguerra: </p>
<hr />
<div>= 3DNA =<br />
<br />
== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36633DNA2008-03-07T00:49:55Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
== Overview ==<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
== Invoking ==<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example 1 ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
== Example 2 ==<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
<gallery><br />
Image:X3dna_r3d_pymol.png<br />
</gallery><br />
<br />
<br />
== More ==<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36623DNA2008-03-07T00:45:52Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example ==<br />
<gallery><br />
Image:trna.png|Using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36613DNA2008-03-07T00:44:51Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example ==<br />
<gallery><br />
Image:trna.png| using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
== Syntax ==<br />
<source lang="python"><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</source><br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36603DNA2008-03-07T00:42:43Z<p>Esguerra: /* Example */</p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example ==<br />
<gallery><br />
Image:trna.png| using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36593DNA2008-03-07T00:42:30Z<p>Esguerra: /* Example */</p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example ==<br />
<gallery><br />
Image:trna.png| using tb.pdb<br />
and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36583DNA2008-03-07T00:40:10Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
== Example ==<br />
<gallery><br />
Image:trna.png| using tb.pdb and t2.r3d<br />
</gallery><br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36573DNA2008-03-07T00:36:50Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> from 3DNA v. 2.0 directly. Using the following command:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36563DNA2008-03-07T00:34:10Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed, and the path to their binaries correctly configured, you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36553DNA2008-03-07T00:33:36Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA[http://3dna.rutgers.edu] provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36543DNA2008-03-07T00:32:23Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]<br />
<br />
<br />
More examples of figures obtained using 3DNA for preprocessing can be found at:<br />
<br />
[[http://www.eden.rutgers.edu/~esguerra/CHEMISTRY/nucleic_acids.html]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36533DNA2008-03-07T00:28:41Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:X3dna_r3d_pymol.png]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=File:X3dna_r3d_pymol.png&diff=2899File:X3dna r3d pymol.png2008-03-07T00:27:27Z<p>Esguerra: </p>
<hr />
<div></div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36523DNA2008-03-07T00:26:04Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre><br />
<br />
And the result is:<br />
<br />
[[Image:Example.jpg]]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36513DNA2008-03-07T00:02:33Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster3D format, and are also processed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre></div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36503DNA2008-03-07T00:01:56Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids. The produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre></div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36493DNA2008-03-07T00:00:30Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
<br />
[[Image:trna.png]]<br />
<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre></div>Esguerrahttps://wiki.pymol.org/index.php?title=File:Trna.png&diff=2874File:Trna.png2008-03-06T23:59:17Z<p>Esguerra: </p>
<hr />
<div></div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36483DNA2008-03-06T23:58:34Z<p>Esguerra: </p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
[[Image:trna.png]]<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
load tb.pdb<br />
load t2.r3d<br />
bg_color white<br />
hide lines<br />
zoom *,-5<br />
set ray_trace_mode, 3<br />
set ray_trace_fog, 0<br />
sert ray_shadows, 0<br />
set orthoscopic, 1<br />
set antialias, 5<br />
set valence, 1<br />
util.cba(29)<br />
color grey, (elem C)<br />
cartoon arrow<br />
set cartoon_ladder_mode, 0<br />
set cartoon_rect_width, 0.2<br />
set cartoon_rect_length, 0.5<br />
show cartoon<br />
set stick_radius, 0.14<br />
show sticks<br />
set_view (\<br />
0.680474579, -0.153203458, -0.716576934,\<br />
0.658882320, -0.300013036, 0.689829707,\<br />
-0.320666909, -0.941552401, -0.103208199,\<br />
-0.000084338, 0.000022471, -263.030426025,\<br />
57.723434448, 45.338260651, 20.895099640,\<br />
218.710235596, 307.348541260, 1.000000000 )<br />
set cartoon_color, green, resn G<br />
set cartoon_color, yellow, resn C<br />
set cartoon_color, red, resn A<br />
set cartoon_color, cyan, resn U<br />
ray 1024,768<br />
png trna.png<br />
quit<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre></div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36473DNA2008-03-06T23:57:36Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)<br />
<br />
<pre> <br />
pdb_get.py 1ehz<br />
blocview -o 1ehz.pdb<br />
</pre><br />
<br />
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py]<br />
<br />
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:<br />
<br />
[[Image:Example.jpg]]<br />
<br />
To generate the previous image the following script was used:<br />
trna.pml<br />
<br />
<pre><br />
<br />
</pre><br />
<br />
<br />
An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way:<br />
<br />
<pre><br />
blocview -o -t=100 1ehz.pdb<br />
</pre></div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36463DNA2008-03-06T22:11:52Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]<br />
<br />
Once you have the previous software installed and the path to their binaries correctly configured you just need to run from a terminal window:<br />
<br />
<pre> <br />
blocview -o pdbfile.pdb<br />
</pre></div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36453DNA2008-03-06T22:07:24Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
<br />
<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0 [http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36443DNA2008-03-06T22:04:59Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
<br />
<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- <a href="http://rutchem.rutgers.edu/~xiangjun/3DNA">3DNA V1.5</a>[http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0[http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36433DNA2008-03-06T22:03:13Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
<br />
<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA V1.5[http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
<br />
- 3DNA V2.0[http://3dna.rutgers.edu/]<br />
<br />
- Raster 3D [http://skuld.bmsc.washington.edu/raster3d/raster3d.html]<br />
<br />
- Molscript [http://www.avatar.se/molscript/download.html]</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36423DNA2008-03-06T22:01:02Z<p>Esguerra: /* 3DNA */</p>
<hr />
<div>== 3DNA ==<br />
<br />
<br />
<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
- Raster 3D<br />
- Molscript</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36413DNA2008-03-06T22:00:50Z<p>Esguerra: /* '''3DNA''' */</p>
<hr />
<div>== 3DNA ==<br />
<br />
<br />
----<br />
<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
- Raster 3D<br />
- Molscript</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36403DNA2008-03-06T22:00:21Z<p>Esguerra: </p>
<hr />
<div>== '''3DNA''' ==<br />
<br />
<br />
----<br />
<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
- Raster 3D<br />
- Molscript</div>Esguerrahttps://wiki.pymol.org/index.php?title=3DNA&diff=36393DNA2008-03-06T21:59:58Z<p>Esguerra: New page: 3DNA ---- 3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster...</p>
<hr />
<div>3DNA<br />
<br />
----<br />
<br />
<br />
3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:<br />
<br />
- 3DNA [http://rutchem.rutgers.edu/~xiangjun/3DNA] <br />
- Raster 3D<br />
- Molscript</div>Esguerra