pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Tobias -
It seems to me that you may not have hidden the lines/sticks from the object where you’ve shown the surface. For overlapping objects, the normal non-ray-traced view appears to give precedence to the object that was present in the viewer first. Try disabling and re-enabling your two objects in different orders to see what I mean. Ray, on the other hand, tries to show both at the same time.
There is actually another way to accomplish what you describe in (b). First, you can use the `surface_mode` setting (http://pymolwiki.org/index.php/Surface_mode) to avoid having to modify the flags. Also, instead of creating two objects, the easiest way to have different colors for the surface and the sticks is to use the `surface_color` setting (http://pymolwiki.org/index.php/Surface_color) for your ligand object.
set surface_mode, 1
set transparency, 0.5
as sticks, ligand
show surface, ligand
set surface_color, black, ligand
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On Mar 31, 2014, at 8:42 AM, Tobias Beck <tob...@gm...<mailto:tob...@gm...>> wrote:
Dear all,
I would like to show a transparent surface of a ligand, with the ligand 'inside' as sticks.
I created a new object of the ligand, then tried to show the surface, which fails.
With this information here: http://sourceforge.net/p/pymol/mailman/message/27299068/
# do not ignore surfacing of ligands
flag ignore, not rep surface
# force PyMOL to rebuild the surface
rebuild
I was then able to show the surface of the ligand. All colors are fine. Transparency is set to 0.5
Now I would like to create an image with ray. However, after ray, there are problems with the color of the ligand sticks inside:
a) if the ligand is green and the surface is black, the ligand sticks inside are black as well
b) if the surface is black and the ligand carbon atoms are shown in green and other atoms colored by 'color by element', then the non-carbon atoms have their native color with pixels of black (surface color) covering them....
I would like to get b) to work. Any suggestions? Do the commands above (flag ignore) change something for ray?
For other surfaces (protein), the above works fine, without any pixels of surface color on the non-carbon atoms.
Thank you and best wishes, Tobias.
--
_______________________________________
Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Vladimir-Prelog-Weg 3, HCI F 322
8093 Zurich, Switzerland
phone: +41 44 632 68 65
fax: +41 44 632 14 86
web: http://www.protein.ethz.ch/people/tobias
_______________________________________
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Hi Kelvin,
the "psico" module provides a "fasta" command which maintains the gaps. However, psico will not work with PyMOL 0.99 which is quite old and uses an ancient Python version (psico requires Python 2.6 and and the PyMOL 1.2 API).
Psico installations instructions and download link:
http://pymolwiki.org/index.php/Psico
Cheers,
 Thomas
On 31 Mar 2014, at 05:13, Kelvin Luther <kl...@ac...> wrote:
> Hello,
> 
> I am using PyMOL 0.99rc6. I am wondering if there is a means to obtain 
> a FASTA sequence from a loaded pdb file that maintains the gaps due to 
> missing portions of the structure? I found one program that will strip 
> the sequence from pdb files, but it simply reads out the amino acids 
> that are present linearly. Gaps in the sequence are not maintained. I 
> can't imagine why that would be useful. I have a large number of pdb 
> files to deal with and would like to avoid having to align each pdb 
> sequence to the gene just to recover the gaps.
> 
> Thanks for your time,
> 
> -- 
> Kelvin Luther
> Physiologische Institut
> Universität Zürich
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Due to the possibility of insertion codes and non-sequential residue numbering,
I believe there is no way to avoid aligning the residues in the ATOM records
with the sequence in SEQRES in order to find gaps. I don't know of a program
to do this.
The structure validation server at RCSB ADIT2 makes this alignment for the
depositor to look at, but it would not be easy to include in a script.
If all you want are "accurate fasta sequence" for the the protein
there are programs to convert the SEQRES records to a string of
one-letter codes. The SEQRES record in principle has the sequence
of what is present in the crystal, regardless of whether it is
visualized or not. However there cannot be conflicts between the
SEQRES and the atom records, so if the structure contains
unknown ('UNK') residues, they have to be UNK in the SEQRES also,
even if the sequence is known. And if a string of UNK residues is
disconnected on both ends, i.e. in the middle of a gap of missing
residues, then it is pretty arbitrary which residues in seqres get
replaced with UNK.
Kelvin Luther wrote:
> Hello,
>
> I am using PyMOL 0.99rc6. I am wondering if there is a means to obtain
> a FASTA sequence from a loaded pdb file that maintains the gaps due to
> missing portions of the structure? I found one program that will strip
> the sequence from pdb files, but it simply reads out the amino acids
> that are present linearly. Gaps in the sequence are not maintained. I
> can't imagine why that would be useful. I have a large number of pdb
> files to deal with and would like to avoid having to align each pdb
> sequence to the gene just to recover the gaps.
>
> Thanks for your time,
>

Dear all,
I would like to show a transparent surface of a ligand, with the ligand
'inside' as sticks.
I created a new object of the ligand, then tried to show the surface, which
fails.
With this information here:
http://sourceforge.net/p/pymol/mailman/message/27299068/
# do not ignore surfacing of ligands
flag ignore, not rep surface
# force PyMOL to rebuild the surface
rebuild
I was then able to show the surface of the ligand. All colors are fine.
Transparency is set to 0.5
Now I would like to create an image with ray. However, after ray, there are
problems with the color of the ligand sticks inside:
a) if the ligand is green and the surface is black, the ligand sticks
inside are black as well
b) if the surface is black and the ligand carbon atoms are shown in green
and other atoms colored by 'color by element', then the non-carbon atoms
have their native color with pixels of black (surface color) covering
them....
I would like to get b) to work. Any suggestions? Do the commands above
(flag ignore) change something for ray?
For other surfaces (protein), the above works fine, without any pixels of
surface color on the non-carbon atoms.
Thank you and best wishes, Tobias.
-- 
_______________________________________
Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Vladimir-Prelog-Weg 3, HCI F 322
8093 Zurich, Switzerland
phone: +41 44 632 68 65
fax: +41 44 632 14 86
web: http://www.protein.ethz.ch/people/tobias
_______________________________________

Hello,
I am using PyMOL 0.99rc6. I am wondering if there is a means to obtain 
a FASTA sequence from a loaded pdb file that maintains the gaps due to 
missing portions of the structure? I found one program that will strip 
the sequence from pdb files, but it simply reads out the amino acids 
that are present linearly. Gaps in the sequence are not maintained. I 
can't imagine why that would be useful. I have a large number of pdb 
files to deal with and would like to avoid having to align each pdb 
sequence to the gene just to recover the gaps.
Thanks for your time,
-- 
Kelvin Luther
Physiologische Institut
Universität Zürich

Hi there,
I am trying to plot a series of clipping slabs through a protein 
structure, but would like to show an additional figure to indicate where 
the 'slices' are from (similar to what you would do with a MRI or 
CT-scan in medicine - something akin to ' 
http://lmi.bwh.harvard.edu/papers/pictures/2003/frimanThesis03/frimanThesis03.png 
' ). I have searched for the last few days and cannot seem to find 
anything simple to do this task. Does anyone know if there is a small 
script somewhere that can plot a 'plane' as defined by the clipping slab?
Cheers,
Tom
-- 
*Thomas J Carruthers *
Structural Biology and Biophysics
Research School of Chemistry
Australian National University

Hi Durga,
it looks like you haven't loaded the PyDeT plugin. Instead of tracking the problem down or fixing PyDeT, I can offer a different script that I wrote. If you run the script, it adds a "delaunay" command. You need to have the "qdelaunay" executable installed on your system.
Download the script:
https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/geometry.py
Example:
PyMOL> fetch 1ubq, async=0
PyMOL> run geometry.py
PyMOL> delaunay name CA
Hope that helps.
Cheers,
 Thomas
On 25 Mar 2014, at 15:23, KanakaDurga Addepalli <kad...@ma...> wrote:
> Hi,
> I am a total newbie and just want to get some delaunay images for my proteins using PyDeT.
> 
> I am trying to get the PyDeT plugin to work since yday but it throws up an exception
> 
> PyMOL>pydet pt, name c
> Traceback (most recent call last):
> File "/Volumes/Data/scm/vikki/bld/MacPyMOL.app/pymol/modules/pymol/parser.py", line 464, in parse
> File "<string>", line 1
> pydet pt, name c
> 
> Could you please help,
> thanks.
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi,
I am a total newbie and just want to get some delaunay images for my proteins using PyDeT.
I am trying to get the PyDeT plugin to work since yday but it throws up an exception
PyMOL>pydet pt, name c
Traceback (most recent call last):
 File "/Volumes/Data/scm/vikki/bld/MacPyMOL.app/pymol/modules/pymol/parser.py", line 464, in parse
 File "<string>", line 1
 pydet pt, name c
Could you please help,
thanks.

Hi Jordan,
there is unfortunately no way to exclude the labels from the "ray_trace_mode > 0" outlines. You might want to create two images, one without labels and one with labels only. See this post which asked the same question:
http://sourceforge.net/p/pymol/mailman/message/28232197/
Cheers,
 Thomas
> From: Jordan Willis <jwi...@gm...>
> Subject: Label outline dominates label interior
> Date: 24 Mar 2014 20:26:34 EDT
> 
> I was trying to make colored labels. Of course you can just use 
> 
> set label_color, my_label, my_color
> 
> However, there still is a black outline. When you ray-trace this, it dominates the color so you can’t see it. I tried changing the label outlines to the same color as the interior, but black still dominates.
> 
> No matter what I’ve tried (white outlines, different fonts, ray-traced modes), a ray traced representation always shows a black dominated label. See picture attached (ray_trace_mode, 4) 
> 
> Is there something I’m missing? I’m using Pymol 1.7 for mac.
> 
> Jordan
> 
> <forgroup.png>
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

On Mon, Mar 24, 2014 at 05:46:15AM -0400, David Hall wrote:
> Not sure if the git svn stopping at rev 3938 was a question, but maybe you are using the old svn URL?
> 
> svn://svn.code.sf.net/p/pymol/code/
> 
Sorry - I was unclear - I did not mean the revisions stopped there just that I observed
there are no changes involving the noInvalidateMMStereoAndTextType flag after that revision
- it was also created in that revision
Thanks for the tip - my git clone is using the above url as the svn remote
David

Not sure if the git svn stopping at rev 3938 was a question, but maybe you are using the old svn URL?
svn://svn.code.sf.net/p/pymol/code/
Should get you up to date
-David
> On Mar 23, 2014, at 10:18 PM, David Osguthorpe <dav...@gm...> wrote:
> 
>> On Sun, Mar 23, 2014 at 06:02:32PM -0400, Thomas Holder wrote:
>> Hi David,
>> 
>> very well analyzed. You are right that noInvalidateMMStereoAndTextType should never be set to 0 in the open-source version, we will fix that.
>> 
>> FYI: The incentive version of PyMOL can use a proprietary Schrödinger library to assign text_type and stereochemistry, in which case that flag is used.
> 
> Thanks for the update - it just didnt look right - I can see having a function to clear it and set it
> (I noticed you can set text_type with alter)
> - and its not consistent with numeric/custom type which also seemed to be associated with potential type
> but it didnt make sense that in order to see the type field you would need to read the mol2 in, then
> have an extension command which re-parses the mol2 file and set it using alter
> 
> (Ive found using git svn works nicely - Im getting used to git for many other systems including my old fortran
> sources previously in RCS/CVS
> - which allowed me to track the update to the svn revision 3938 PyMOL version 1.4b1 - and no changes since then)
> 
> 
> David
> 
> ------------------------------------------------------------------------------
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> PyMOL-users mailing list (PyM...@li...)
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> Archives: http://www.mail-archive.com/pym...@li...

On Sun, Mar 23, 2014 at 06:02:32PM -0400, Thomas Holder wrote:
> Hi David,
> 
> very well analyzed. You are right that noInvalidateMMStereoAndTextType should never be set to 0 in the open-source version, we will fix that.
> 
> FYI: The incentive version of PyMOL can use a proprietary Schrödinger library to assign text_type and stereochemistry, in which case that flag is used.
> 
Thanks for the update - it just didnt look right - I can see having a function to clear it and set it
(I noticed you can set text_type with alter)
- and its not consistent with numeric/custom type which also seemed to be associated with potential type
but it didnt make sense that in order to see the type field you would need to read the mol2 in, then
have an extension command which re-parses the mol2 file and set it using alter
(Ive found using git svn works nicely - Im getting used to git for many other systems including my old fortran
sources previously in RCS/CVS
- which allowed me to track the update to the svn revision 3938 PyMOL version 1.4b1 - and no changes since then)
David

Hi David,
very well analyzed. You are right that noInvalidateMMStereoAndTextType should never be set to 0 in the open-source version, we will fix that.
FYI: The incentive version of PyMOL can use a proprietary Schrödinger library to assign text_type and stereochemistry, in which case that flag is used.
Cheers,
 Thomas
On 21 Mar 2014, at 14:04, David Osguthorpe <dav...@gm...> wrote:
> Does anybody have a clue what this flag (noInvalidateMMStereoAndTextType) is doing?
> 
> I was using openbabel to minimize a molecule and trying to figure out how it
> was parameterising some nitrogens (sp2/sp3 for nitrogens is always a problem as they
> both have 3 bonds) (mmff94).
> 
> I wrote out the molecule as MOL2 where there is a field for type (some form of potential type).
> But when displayed in pymol this field was blank.
> 
> I tracked this down to this flag noInvalidateMMStereoAndTextType - when reading this flag
> is set to 1 before the call to ObjectMoleculeMOL2SetFormalCharges which sets it back
> to 0 at end of this routine.
> Then at end of reading there is a call to ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1);
> which blanks textType - hence display of null string.
> 
> I then tried setting text_type in a chempy model and using load_model
> - from this found that noInvalidateMMStereoAndTextType is set to 0 in CoordSetNew
> - and again the seemingly obligatory ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1);
> at end of reading clobbers any input data.
> 
> For the moment Im setting the flag to 1 in CoordSetNew and commenting assigns to 0
> - then input textType fields are displayed.
> 
> I just cant figure out what this was supposed to be doing - it just doesnt seem
> right that input data of this type is being clobbered.
> 
> Thanks for any info
> 
> David
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Jordan,
multi-line labels are implemented in Incentive PyMOL 1.7, along with other label improvements (see http://pymol.org/dsc/dokuwiki/doku.php?id=setting:label). Those new label features are not in the open-source version so far.
So the labelling that Andreas asked for in 2011 can now be done by:
PyMOL> label all, resn.capitalize() + resi + "\n%.1f" % b
PyMOL> set label_multiline_justification, 0
Cheers,
 Thomas
On 23 Mar 2014, at 00:01, Jordan Willis <jwi...@gm...> wrote:
> Hi,
> 
> I stumbled across this email:
> 
> https://www.mail-archive.com/pym...@li.../msg08945.html
> 
> Wondering if it was still unimplemented or if I’m missing it somewhere
> 
> Jordan
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi,
I stumbled across this email:
https://www.mail-archive.com/pym...@li.../msg08945.html
Wondering if it was still unimplemented or if I’m missing it somewhere
Jordan

Hi Jared,Thank you so much for your help - this was driving me crazy for hours! I used your first solution to keep everything as a single chain, and it worked perfectly. Again, many thanks for your help.Nick.
> From: Jar...@ny...
> To: wi...@ho...
> CC: pym...@li...
> Subject: Re: [PyMOL] Pymol insertion code
> Date: 2014年3月20日 17:26:21 +0000
> 
> Sorry - one quick correction to my previous email:
> 
> On Mar 20, 2014, at 10:50 AM, Sampson, Jared <Jar...@ny...> wrote:
> 
> > If you don’t need the cartoon representation to be continuous (e.g. if you’re zooming in on a different section of the protein you can replace the 3rd line with:
> > 
> > alter prodomain, chain="P"
> > 
> > to split off the prodomain into a separate chain. In this case, the sequence will be numbered as in the PDB, only without the insertion code.
> 
> The numbering will be exactly as in the PDB, only the chain ID will differ.
> 
> Cheers,
> Jared
> 
> 
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
> =================================
> 
 		 	 		 

Does anybody have a clue what this flag (noInvalidateMMStereoAndTextType) is doing?
I was using openbabel to minimize a molecule and trying to figure out how it
was parameterising some nitrogens (sp2/sp3 for nitrogens is always a problem as they
both have 3 bonds) (mmff94).
I wrote out the molecule as MOL2 where there is a field for type (some form of potential type).
But when displayed in pymol this field was blank.
I tracked this down to this flag noInvalidateMMStereoAndTextType - when reading this flag
is set to 1 before the call to ObjectMoleculeMOL2SetFormalCharges which sets it back
to 0 at end of this routine.
Then at end of reading there is a call to ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1);
which blanks textType - hence display of null string.
I then tried setting text_type in a chempy model and using load_model
- from this found that noInvalidateMMStereoAndTextType is set to 0 in CoordSetNew
- and again the seemingly obligatory ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1);
at end of reading clobbers any input data.
For the moment Im setting the flag to 1 in CoordSetNew and commenting assigns to 0
- then input textType fields are displayed.
I just cant figure out what this was supposed to be doing - it just doesnt seem
right that input data of this type is being clobbered.
Thanks for any info
David

Good!
Responding to my question, It's possible also into the open-source PyMOL
version: I found
this<https://www.mail-archive.com/pym...@li.../msg07951.html>topic.
You need to *duplicate *the pdb entry as *object*, and apply
"*cartoon_side_chain_helper
= off*" to the first object and "*cartoon_side_chain_helper = on*" to its
copy (or *vice versa*), selecting the residues of each entry, in this way,
for example:
cmd.fetch("1qpe", async=0);
cmd.remove("(solvent and (all))");
cmd.create("1qpe_copy","1qpe");
cmd.hide("everything","1qpe_copy");
cmd.show_as("cartoon","1qpe");
cmd.show("sticks","/1qpe//A/316+317+319");
cmd.set("cartoon_side_chain_helper", "off", "1qpe");
cmd.show_as("cartoon","1qpe_copy");
cmd.show("sticks","/1qpe_copy//A/393+394+395");
cmd.set("cartoon_side_chain_helper", "on", "1qpe_copy");
Cheers,
Riccardo
 *ChemBioScripting | X3D PyMOL Molecule Viewer
<http://chembioscripting.hol.es> *|* Gioacchino Riccardo Volpe*
2014年03月20日 22:17 GMT+01:00 Riccardo <mi...@gm...>:
> Hi Tsjerk!
>
> So, Yes! Thanks to visit my website!! :)... I understand where is the
> problem! I created that website before have a mobile device :), as
> experiment to get the fantastic PyMOL rendering in an interactive 3D web
> environment, so it's expressly designed for a desktop computer, and I'm not
> sure how good it looks on a tablet! I need and want to rewrite it, making
> it responsive for mobile devices too: for now, it works well only on web
> browser for computer desktop, like Chrome or Firefox... Sorry for the
> inconvenience, but before rewrite it, I thought to add some tasks to it for
> a next version, like download pdb files from Protein Data Bank, for which
> I'm writing some python code at moment.
>
> In the meantime, I will translate buttons and other explainations in
> english, if you want, but I suggest you to visit it on a computer desktop
> with web browser like Chrome or Firefox or Opera (with supported and
> enabled WebGL: Safari supports WebGL only in Mac version, not in its
> Windows Version); for Microsoft Internet Explorer, only IE11 (in Windows
> 8.1) supports WebGL natively, without external plugins.
>
> Thanks :),
>
> Greetings,
> Riccardo
>
>
> *ChemBioScripting | X3D PyMOL Molecule Viewer
> <http://chembioscripting.hol.es> *|* Gioacchino Riccardo Volpe*
>
>
> 2014年03月20日 20:46 GMT+01:00 Tsjerk Wassenaar <ts...@gm...>:
>
> Hey Riccardo,
>>
>> I clicked on the link on my Nexus 7. It opened the viewer with a protein
>> loaded, and gave very nice response to multi touch gestures. But there were
>> two buttons in the middle of the view, like > and <. So I pressed > and
>> that made a sort of menu pop up from the side with what looked as some kind
>> of controls. But that was in Italian :p
>>
>> Cheers,
>>
>> Tsjerk
>> On Mar 20, 2014 7:40 PM, "Riccardo" <mi...@gm...> wrote:
>>
>>> Hi Tsjerk,
>>>
>>> Glad to hear a greeting in Italian! :) ...
>>>
>>> Sorry for the question, but I'm not sure about what do you refear
>>> speaking of "buttons"... Are you speaking about my website? The only
>>> Italian "buttons", in this context, are probably those on my website...
>>> Have you saw it on a tablet?
>>>
>>> Cheers,
>>> Riccardo
>>>
>>
>

Sorry - one quick correction to my previous email:
On Mar 20, 2014, at 10:50 AM, Sampson, Jared <Jar...@ny...> wrote:
> If you don’t need the cartoon representation to be continuous (e.g. if you’re zooming in on a different section of the protein you can replace the 3rd line with:
> 
> alter prodomain, chain="P"
> 
> to split off the prodomain into a separate chain. In this case, the sequence will be numbered as in the PDB, only without the insertion code.
The numbering will be exactly as in the PDB, only the chain ID will differ.
Cheers,
Jared
------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

Hi Riccardo,
cartoon_side_chain_helper has been implemented as an atom level setting only in the latest Incentive version of PyMOL (1.7.0.0 Incentive PyMOL).
Cheers,
 Thomas
On 20 Mar 2014, at 12:05, Riccardo <mi...@gm...> wrote:
> Hello to PyMOL mailing list.
> 
> I'm writing a python script using PyMOL as module.
> 
> I want to set "cartoon_side_chain_helpe = on" globally and, only for residues inside a list (chosen_residues_replacement_list), I want to set "cartoon_side_chain_helpe = off".
> 
> For this purpuse, I'm trying to use "unset" in this way:
> 
> ## Choice:
> chosen_residues = "316+317+319";
> 
> ## Task:
> chosen_residues_replacement = chosen_residues.replace("+", " ");
> chosen_residues_replacement_list = chosen_residues_replacement.split();
> if not chosen_residues_replacement_list:
> print("Empty list!");
> else:
> residues = "resi {}".format(chosen_residues);
> cmd.select("residues", residues, enable=1);
> cmd.select("everything_else","(not residues)", enable=1); # invert "residues" selection
> cmd.set("cartoon_side_chain_helper", "on");
> cmd.unset("cartoon_side_chain_helper","residues");
> 
> but in this way I can't see "cartoon_side_chain_helper = off" for residues in "chosen_residues".
> 
> Thanks a lot,
> Riccardo Volpe
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hello to PyMOL mailing list.
I'm writing a python script using PyMOL as module.
I want to set "*cartoon_side_chain_helpe = on*" globally and, only for
residues inside a list (*chosen_residues_replacement_list*), I want to
set "*cartoon_side_chain_helpe
= off*".
For this purpuse, I'm trying to use
"unset<http://www.pymolwiki.org/index.php/Unset>"
in this way:
*## Choice:*
chosen_residues = "316+317+319";
*## Task:*
chosen_residues_replacement = chosen_residues.replace("+", " ");
chosen_residues_replacement_list = chosen_residues_replacement.split();
if not chosen_residues_replacement_list:
 print("Empty list!");
else:
 residues = "resi {}".format(chosen_residues);
 cmd.select("residues", residues, enable=1);
 cmd.select("everything_else","(not residues)", enable=1); # invert
"residues" selection
 cmd.set("cartoon_side_chain_helper", "on");
 cmd.unset("cartoon_side_chain_helper","residues");
but in this way I can't see "*cartoon_side_chain_helper = off*" for
residues in "*chosen_residues*".
Thanks a lot,
Riccardo Volpe
 *ChemBioScripting | X3D PyMOL Molecule Viewer
<http://chembioscripting.hol.es> *|* Gioacchino Riccardo Volpe*

Hi Nick -
This PDB employs non-standard usage of the PDB insertion code column. Typically, it is used to insert one or more residues between adjacent numbers in a canonically numbered structure, e.g. residue 42A (along with 42B, 42C, ... , 42P, etc.) is between residues 42 and 43.
As for whether it affects the structure: Yes, in this case, this non-standard usage also has the unwanted side effect in PyMOL of preventing the prodomain from being shown in cartoon representation, because its residues are too far from "adjacent" residues (i.e. the mature peptide residues with numbers on either side of the "inserted" residue).
To view the sequences as intended while keeping the mature peptide numbering the same, try this:
fetch 3psg, async=0
select prodomain, resi *P
alter prodomain, resi=str(int(resi[:-1])-44) # decrement integer portion of prodomain residues by 44
sort
With this method (as opposed to extracting the prodomain to a new chain or object), you get a continuous cartoon based on atom connectivity. The drawback is, if you need to refer to specific residues of the prodomain, you have to do a little math.
If you don’t need the cartoon representation to be continuous (e.g. if you’re zooming in on a different section of the protein you can replace the 3rd line with:
alter prodomain, chain="P"
to split off the prodomain into a separate chain. In this case, the sequence will be numbered as in the PDB, only without the insertion code.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On Mar 20, 2014, at 8:59 AM, Wimock <wi...@ho...<mailto:wi...@ho...>> wrote:
Hi,
I'm new to Pymol and am looking at the structure of pepsinogen (PDB: 3psg). This protein contains a 44 residue prodomain, which the pdb file says is assigned an insertion code 'P' and labelled 1 - 44. This prodomain is cleaved to yield pepsin (5pep), whose sequence is labelled 1 - 326. I gather Pymol should be able to see these as separate parts of the sequence, but it instead seems to interleave the sequences - I don't know if this affects the structure or not? Other programs (Chimera) show the sequence as it should be (P1-44...1-326).
Is there a way to have the sequence parts recognised in the sequence viewer? This would make it much easier for me to manipulate these sections. Please let me know if I haven't been clear.
Thanks,
Nick.
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Hi,
I'm new to Pymol and am looking at the structure of pepsinogen (PDB: 3psg). This protein contains a 44 residue prodomain, which the pdb file says is assigned an insertion code 'P' and labelled 1 - 44. This prodomain is cleaved to yield pepsin (5pep), whose sequence is labelled 1 - 326. I gather Pymol should be able to see these as separate parts of the sequence, but it instead seems to interleave the sequences - I don't know if this affects the structure or not? Other programs (Chimera) show the sequence as it should be (P1-44...1-326).
Is there a way to have the sequence parts recognised in the sequence viewer? This would make it much easier for me to manipulate these sections. Please let me know if I haven't been clear.
Thanks,Nick. 		 	 		 

Hi Chandan - Back in the lab today. I took a look at the code I sent and realized that one can’t simply pass a tuple to cmd.color(), as it only accepts named colors, so you have to use cmd.set_color().
So here (below) is a modified, fleshed-out version of what I sent yesterday, with the protein components of the T. thermophilus ribosome asymmetric unit (110 chains) as an example. For a larger number of colors, you would simply have to increase the ranges for i, j, and k in the loop that creates the RGB tuples.
Some of the colors turn out to be fairly similar (e.g. those differing by only one RGB component), so also maybe check out, e.g., this SO question and its answers for alternative approaches: http://stackoverflow.com/questions/470690/how-to-automatically-generate-n-distinct-colors.
Cheers,
Jared
###
from pymol import cmd
from random import shuffle
cmd.fetch("2wdk", async=0)
cmd.fetch("2wdl", async=0)
cmd.fetch("2wdm", async=0)
cmd.fetch("2wdn", async=0)
# remove non-polymer components so we can just view the cartoon
cmd.remove("all and not polymer")
# remove RNA chains to get a better view of individual protein chains
cmd.remove("chain A")
my_chains = []
for obj in cmd.get_names():
 for ch in cmd.get_chains(obj):
 my_chains.append((obj, ch))
print "There are currently %s chains to be colored." % len(my_chains)
my_colors = []
# 5^3 > 100
for i in range (0, 5):
 r = 0.25 * i
 for j in range (0, 5):
 g = 0.25 * j
 for k in range (0, 5):
 b = 0.25 * k
 my_colors.append([r, g, b])
# randomize list (optional)
shuffle(my_colors)
print "shuffled the colors"
# name the colors
for i, tup in enumerate(my_colors):
 cmd.set_color("mycolor_%s" % i, "%s" % tup)
 print "set color mycolor_%s to %s" % (i, tup)
# color your chains
for i, ch in enumerate(my_chains):
 sel = "%s and chain %s" % (ch[0], ch[1])
 color = "mycolor_%s" % i
 color_tuple = my_colors[i]
 print "%s will be colored %s (%s)" % (sel, color, color_tuple)
 cmd.color("%s" % color, sel)
###
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On Mar 17, 2014, at 2:07 PM, Sampson, Jared <Jar...@ny...<mailto:Jar...@ny...>> wrote:
Hi Chandan -
It seems like you're being limited by the 26 numbered colors in the util.cbc function. You could create your own randomized list of evenly-spaced colors, something like the following (untested, but should be approximately usable--sorry, I'm away from my computer today):
from pymol import cmd
from random import shuffle
my_colors = []
# 5^3 > 100
for i in range (0, 5):
 r = 0.25 * i
 for j in range (0, 5):
 g = 0.25 * j
 for k in range (0, 5):
 b = 0.25 * k
 my_colors.append([r, g, b])
# randomize list
shuffle(my_colors)
# color your chains
for x, c in enumerate(my_chain_list):
 cmd.color(my_colors[x], c)
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Kong Lab
NYU Medical Center
kong.med.nyu.edu<http://kong.med.nyu.edu>
212-263-7898
Sent from my iPhone
On Mar 17, 2014, at 8:37 AM, "Thomas Holder" <tho...@sc...> wrote:
Hi Chandan,
in Incentive PyMOL 1.6 you can use the spectrum command to color by chain (will be enumerated) or by residue number. http://pymolwiki.org/index.php/Spectrum
In open-source PyMOL, you could use the spectrumany script to color by residue number: http://pymolwiki.org/index.php/Spectrumany
Cheers,
Thomas
On 13 Mar 2014, at 03:19, Chandan Choudhury <ii...@gm...> wrote:
On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis <jwi...@gm...> wrote:
I think...
What is happening is that the color command should take in a name like "color yellow, i. 1" or a CMYK color vector. When you are saying "color 1" it is just starting at the first index of CMYK which is black.
There is a command for your problem though. Just say util.color_chains() and it will color all individual chains a different color.
Thanks Jordon for the reply.
I tried using util.color_chains(). It colors differently upto chain no. 26. After 26 all the chains are of same color, as I donot have chain no after that.
Some utility which can color by residue number would be very useful.
Chandan
On Mar 12, 2014, at 11:15 PM, Chandan Choudhury <ii...@gm...> wrote:
Dear PyMOL users,
I build 100 chains of polymer in a box. Residue number is different for every chain. Chain 1 hasresidue no. 1, chain 2 has residue no. 2 and so on. I want to color each chain differently.
So, I wrote a script which generates a pml file, and opening this pml file with PyMOL should color each chain differently.
##color.pml
load 128md_c.pdb
select 1, i. 1
color 1, i. 1
select 2, i. 2
color 2, i. 2
select 3, i. 3
color 3, i. 3
select 4, i. 4
color 4, i. 4
select 5, i. 5
color 5, i. 5
select 6, i. 6
color 6, i. 6
select 7, i. 7
...
...
color 125, i. 125
select 126, i. 126
color 126, i. 126
select 127, i. 127
color 127, i. 127
select 128, i. 128
color 128, i. 128
I have 128 chains.
What I find that mostly green or black dominates the coloring.
While displaying color by the numeric code, what is the maximum no, after which the color repeats?
Chandan
--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India
--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.
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Dear Colleagues,
This is a reminder for approaching deadline to apply for the CCP4 Crystallographic Summer School to be held in June at APS, near Chicago.
Please see the original announcement below for more details.
We hope to see you at APS in June.
With best wishes,
Garib, Ronan and Nukri
Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...
________________________________
From: Sanishvili, Ruslan [rsa...@an...]
Sent: Monday, February 03, 2014 6:02 PM
To: pym...@li...
Subject: [PyMOL] [ccp4bb] CCP4 crystallographic summer school in USA, at APS, June 24-July 2
Dear Colleagues,
We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at
http://www.ccp4.ac.uk/schools/APS-2014/index.php
Title:"CCP4 crystallographic school: >From data collection to structure refinement and beyond"
Dates: June 24 to July 2.
Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA
The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used.
Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections – lectures, tutorials and hands-on trouble-shooting.
There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions.
Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.
Application: Application deadline is April 11. The application form, the program, contact info and other details can be found at http:http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php>
Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments.
We hope to see you at the school,
Garib, Ronan and Nukri
Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...