pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] How to drag molecule in the pane with pymol

[Luigi M. P. <mar...@pr...>]

Hello,
I have one molecules and I am importing a second one in the same file. The second molecule comes on top of the first one.
How do I drag the second molecule around so that it does not overlap with the first? If I choose 'drag matrix', I can rotate the second molecule in the z axis. How can I move along the x/y axis?
Thank you

[PyMOL] Get list of bound residues for al poses on PyMol

[Luigi M. P. <mar...@pr...>]

I can find the polar contact between my target and a ligand, but is it possible to get a table with all the bound residues and for all the poses, instead of manually finding the involved residues one by one?
Thank you.

Re: [PyMOL] [EXTERNAL] Question about rotation in latest version of Pymol

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Katayoun,

You can use the command turn.
Enter 'help turn' at the PyMOL prompt to get the documentation about how to use it.

Best regards,

Blaine


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Physiology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center, Rm. 466
975 NE 10th Street<https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, BRC 466
Oklahoma City, OK 73104-5419

Central Time Zone (follows Daylight Savings Time)

office: (405) 271-8300   lab: (405) 271-8313

Faculty webpage<https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1>
Director: Laboratory of Biomolecular Structure and Function (X-ray crystallography lab)<https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function>
Ex-chair: SSRL Users Executive Committee<https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members>
Charter member: NIH Maximizing Investigators’ Research Award B (MRAB) Study section<https://public.csr.nih.gov/StudySections/DBIB/MBBC/MRAB>
Guest-editor: Special Issue "Nucleic Acid Crystallography Volume II"<https://www.mdpi.com/journal/crystals/special_issues/Nucleic_Acid_Crystallography> submission deadline June 25, 2024
Co-Chair: Oklahoma Data Science Workshop<https://mediasite.ouhsc.edu/Mediasite/Channel/python>
________________________________
From: Katayoun Etemadi Some Olyayi <ke...@br...>
Sent: Wednesday, November 15, 2023 10:03 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Question about rotation in latest version of Pymol


Hello,



I’m trying to rotate 2 atoms simultaneously in Pymol, mac version. I am able to do that by using the command: “rotate axis, angle, selection”. But any axis that I use, gives out very long bonds that look definitely wrong. Except for doing it manually, (using command key+ left click) are there any other commands I could use?



Thanks,

Katayoun

[PyMOL] Question about rotation in latest version of Pymol

[Katayoun E. S. O. <ke...@br...>]

Hello,

I’m trying to rotate 2 atoms simultaneously in Pymol, mac version. I am able to do that by using the command: “rotate axis, angle, selection”. But any axis that I use, gives out very long bonds that look definitely wrong. Except for doing it manually, (using command key+ left click) are there any other commands I could use?

Thanks,
Katayoun

Re: [PyMOL] Dss when creating movie from dcd traj

[Norbert S. <st...@bb...>]

Hi Effie,

try to load the trajectory with the option discrete=1:

load trajectory.dcd, discrete=1

Best,

Norbert

Am 09.11.2023 um 19:38 schrieb Effie Artikis:
> Hello,
>
> I’ve uploaded my MD simulation and am trying to create a movie but 
> I’ve noticed that when I play the MD simulation, the secondary 
> structure isn’t updated frame by frame. For example, although it is an 
> unfolding simulation the protein maintains the secondary structure of 
> the initial frame throughout the trajectory. Employing the dss command 
> for any frame applies those secondary structural characteristics to 
> the rest of the frames in the trajectory. Is there a way to update the 
> dss for each frame as the simulation plays?
>
> Thanks!
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Dss when creating movie from dcd traj

[Effie A. <ear...@gm...>]

Hello,

I’ve uploaded my MD simulation and am trying to create a movie but I’ve
noticed that when I play the MD simulation, the secondary structure isn’t
updated frame by frame. For example, although it is an unfolding simulation
the protein maintains the secondary structure of the initial frame
throughout the trajectory. Employing the dss command for any frame applies
those secondary structural characteristics to the rest of the frames in the
trajectory. Is there a way to update the dss for each frame as the
simulation plays?

Thanks!

Re: [PyMOL] How to delete/hide unwanted poses in Pymol?

[Norbert S. <st...@bb...>]

Hi Luigi,

that depends on how the data are read into PyMOL and how the coordinate 
files are structured.

For example, if you read in a pdb file ligand1.pdb, which contains this 
ligand with different poses having different residue numbers and next 
you read in a second pdb file for the second ligand, it may work as follows:

load ligand1.pdb
load ligand2.pdb
# delete the unwanted poses
remove not ((ligand1 and resid 3) or (ligand2 and resid 8))
show sticks

or

load ligand1.pdb
load ligand2.pdb
hide everything
# show only the desired poses
show sticks, (ligand1 and resid 3) or (ligand2 and resid 8)

If you need to do this repeatedly with many poses, a convenient way 
would be to write a script that generates objects for each ligand/pose 
and you can toogle them visible via the menu on the right side of the 
PyMOL interface (commands enable and disable).

If you coordinate files are structured in a different way or if all data 
are in one coordinate file, modifications may be necessary. Perhaps you 
need to distinguish the ligands and poses based on residue names (resn) 
and numbers (resi). Google for "pymol selection algebra" and commands 
show, hide, remove, enable, disable.

With more sophisticated script programming, one may automatically 
generate different objects for each pose read from a pdb file.

Best,

Norbert

Am 09.11.2023 um 11:41 schrieb Luigi Marongiu, PhD via PyMOL-users:
> Hello,
> I have several poses from a docking to a protein and I have different 
> ligands to compare.
> I can load on PyMol the different ligands on a same protein file, and 
> I can look at each pose for the different ligands but only, let's say, 
> in sync: pose 1 of ligand 1 together with pose 1 of ligand 2; pose 2 
> of ligand 1 together with pose 2 of ligand 2; and so forth.
> Let's say that I am interested in comparing pose 3 of ligand 1 and 
> pose 8 of ligand 2.
> How can I hide or delete the unwanted poses?
> Thank you.
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubsc

[PyMOL] How to delete/hide unwanted poses in Pymol?

[Luigi M. P. <mar...@pr...>]

Hello,
I have several poses from a docking to a protein and I have different ligands to compare.
I can load on PyMol the different ligands on a same protein file, and I can look at each pose for the different ligands but only, let's say, in sync: pose 1 of ligand 1 together with pose 1 of ligand 2; pose 2 of ligand 1 together with pose 2 of ligand 2; and so forth.
Let's say that I am interested in comparing pose 3 of ligand 1 and pose 8 of ligand 2.
How can I hide or delete the unwanted poses?
Thank you.

Re: [PyMOL] help with PyMOL rename command

[<wd...@li...>]

Thank You a lot indeed explanation ways more clear than the wiki one

https://pymolwiki.org/index.php/Rename  https://pymolwiki.org/index.php/Rename


.... I know I should have tried more

 

Again Thanks

Re: [PyMOL] waterbox visulization in pymol

[Matic K. <Mat...@ki...>]

Hi Yeeun,

could it be that you had orthoscopic view (menu Display>Orthoscopic View) enabled in Pymol and not in VMD?

To see the 'grid' I think you usually need Orthoscopic view. I may be wrong. Try the perspective view if that changes things.
So I think this is just a visualisation artefact and does not affect the simulations (if you plan to do that).

Usually all the water molecules are defined in the input file, so I would guess it is not 'several small waterboxes combined into one'.
You can also check by opening the input file in a advanced text editor (Notepad++, Sublime text, ...) and you will be able to count the molecules and see if there is some symmetry defined (probably not).

Best!
Matic


On 22. 10. 23 08:24, 김예은 wrote:
Dear Pymol,
Hello.
I visualized a water box generated by Charmm-gui in pymol.
[image.png]
There is a grid pattern in the waterbox, so I thought several small waterboxes were generated and combined into one.
However, in VMD software, there is no grid pattern in the same waterbox.
[image.png]
Is there any specific visualization method to show the grid pattern in the waterbox in Pymol?
Or, could I think that several small waterboxes were generated and combined into one?

Sincerely,
Yeeun Kim




_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] waterbox visulization in pymol

[김예은 <ky...@gm...>]

Dear Pymol,
Hello.
I visualized a water box generated by Charmm-gui in pymol.
[image: image.png]
There is a grid pattern in the waterbox, so I thought several small
waterboxes were generated and combined into one.
However, in VMD software, there is no grid pattern in the same waterbox.
[image: image.png]
Is there any specific visualization method to show the grid pattern in the
waterbox in Pymol?
Or, could I think that several small waterboxes were generated and combined
into one?

Sincerely,
Yeeun Kim

Re: [PyMOL] [EXTERNAL] Student version

[Engin Ö. <eo...@uc...>]

As part of a class, my students had to use this link, 
https://pymol.org/edu/ last week, and we had zero problems.


I think the educational licenses are working just fine. At least most of 
the time.


Engin


On 10/6/23 5:13 AM, Thomas Charles Pochapsky wrote:
>
> Blaine,
>
> Thanks!  I'll try that.
>
> Tom
>
> On 10/6/23 5:58 AM, Mooers, Blaine H.M. (HSC) wrote:
>> Hi Tom,
>>
>> An alternative is to be to show  your students how to install 
>> Anaconda and then install open source PyMOL,
>> which lacks a few minor features of the incentive version but has 
>> more features than the student version.
>> https://anaconda.org/conda-forge/pymol-open-source.
>>
>> It is likely that they will need Anaconda in the future to install 
>> other scientific computing software.
>>
>> Best regards,
>>
>> Blaine
>>
>>
>> Blaine Mooers, Ph.D.
>> Associate Professor
>> Department of Biochemistry and Physiology
>> College of Medicine
>> University of Oklahoma Health Sciences Center
>> S.L. Young Biomedical Research Center, Rm. 466
>> 975 NE 10th Street 
>> <https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, 
>> BRC 466
>> Oklahoma City, OK 73104-5419
>>
>> Central Time Zone (follows Daylight Savings Time)
>>
>> office: (405) 271-8300   lab: (405) 271-8313
>>
>> Faculty webpage 
>> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> 
>>
>> Laboratory of Biomolecular Structure and Function (X-ray 
>> crystallography lab) 
>> <https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function>
>> SSRL Users Executive Committee 
>> <https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members>
>>
>> Center,
>> ------------------------------------------------------------------------
>> *From:* Thomas Charles Pochapsky <poc...@br...>
>> *Sent:* Friday, October 6, 2023 4:28 AM
>> *To:* pym...@li... 
>> <pym...@li...>
>> *Subject:* [EXTERNAL] [PyMOL] Student version
>> Hi, all.  Did anybody ever reply about the student version of PyMol
>> downloads?  I use it in my class on a regular basis, but I can no longer
>> find the link on the Schrodinger web site.  There is a free download for
>> Maestro, with which I am unfamiliar.   Is this a replacement?
>>
>> Thanks.  Tom
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: 
>> https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARftZ0q2zg$ 
>> [mail-archive[.]com]
>> Unsubscribe: 
>> https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$ 
>> [sourceforge[.]net]
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

-- 
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu

Re: [PyMOL] Student version

[Roger R. <rro...@co...>]

FYI, Pymol runs nicely on modern Chromebooks. You can install Pymol easily
in the Linux container using *sudo apt install pymol*. I think the latest
apt version is 2.4. CCP4i/Coot also runs nicely in the Linux container.
(I'm using a Lenovo Flex 5i Chromebook, $320, as a test bed. This system
has an Intel i3 CPU.) An Intel Chromebook might be an attractive option for
undergrads for biochemistry classes and/or protein crystallography research
projects. You can install Pymol in Windows with pip as well.

Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University

On Fri, Oct 6, 2023 at 5:49 AM Thomas Charles Pochapsky <
poc...@br...> wrote:

> Hi, all.  Did anybody ever reply about the student version of PyMol
> downloads?  I use it in my class on a regular basis, but I can no longer
> find the link on the Schrodinger web site.  There is a free download for
> Maestro, with which I am unfamiliar.   Is this a replacement?
>
> Thanks.  Tom
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] [EXTERNAL] Student version

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Tom,

An alternative is to be to show  your students how to install Anaconda and then install open source PyMOL,
which lacks a few minor features of the incentive version but has more features than the student version.
https://anaconda.org/conda-forge/pymol-open-source.

It is likely that they will need Anaconda in the future to install other scientific computing software.

Best regards,

Blaine


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Physiology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center, Rm. 466
975 NE 10th Street<https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, BRC 466
Oklahoma City, OK 73104-5419

Central Time Zone (follows Daylight Savings Time)

office: (405) 271-8300   lab: (405) 271-8313

Faculty webpage <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1>
Laboratory of Biomolecular Structure and Function (X-ray crystallography lab)<https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function>
SSRL Users Executive Committee<https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members><https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members>

Center,
________________________________
From: Thomas Charles Pochapsky <poc...@br...>
Sent: Friday, October 6, 2023 4:28 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Student version

Hi, all.  Did anybody ever reply about the student version of PyMol
downloads?  I use it in my class on a regular basis, but I can no longer
find the link on the Schrodinger web site.  There is a free download for
Maestro, with which I am unfamiliar.   Is this a replacement?

Thanks.  Tom



_______________________________________________
PyMOL-users mailing list
Archives: https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARftZ0q2zg$ [mail-archive[.]com]
Unsubscribe: https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$ [sourceforge[.]net]

Re: [PyMOL] [EXTERNAL] Student version

[Thomas C. P. <poc...@br...>]

Blaine,

Thanks!  I'll try that.

Tom

On 10/6/23 5:58 AM, Mooers, Blaine H.M. (HSC) wrote:
> Hi Tom,
>
> An alternative is to be to show  your students how to install Anaconda 
> and then install open source PyMOL,
> which lacks a few minor features of the incentive version but has more 
> features than the student version.
> https://anaconda.org/conda-forge/pymol-open-source 
> <https://anaconda.org/conda-forge/pymol-open-source>.
>
> It is likely that they will need Anaconda in the future to install 
> other scientific computing software.
>
> Best regards,
>
> Blaine
>
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Physiology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center, Rm. 466
> 975 NE 10th Street 
> <https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, 
> BRC 466
> Oklahoma City, OK 73104-5419
>
> Central Time Zone (follows Daylight Savings Time)
>
> office: (405) 271-8300   lab: (405) 271-8313
>
> Faculty webpage 
> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> 
>
> Laboratory of Biomolecular Structure and Function (X-ray 
> crystallography lab) 
> <https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function>
> SSRL Users Executive Committee 
> <https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members>
>
> Center,
> ------------------------------------------------------------------------
> *From:* Thomas Charles Pochapsky <poc...@br...>
> *Sent:* Friday, October 6, 2023 4:28 AM
> *To:* pym...@li... 
> <pym...@li...>
> *Subject:* [EXTERNAL] [PyMOL] Student version
> Hi, all.  Did anybody ever reply about the student version of PyMol
> downloads?  I use it in my class on a regular basis, but I can no longer
> find the link on the Schrodinger web site.  There is a free download for
> Maestro, with which I am unfamiliar.   Is this a replacement?
>
> Thanks.  Tom
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: 
> https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARftZ0q2zg$ 
> <https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARftZ0q2zg$> 
> [mail-archive[.]com]
> Unsubscribe: 
> https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$ 
> <https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$> 
> [sourceforge[.]net]

[PyMOL] Student version

[Thomas C. P. <poc...@br...>]

Hi, all.  Did anybody ever reply about the student version of PyMol 
downloads?  I use it in my class on a regular basis, but I can no longer 
find the link on the Schrodinger web site.  There is a free download for 
Maestro, with which I am unfamiliar.   Is this a replacement?

Thanks.  Tom

Re: [PyMOL] Changing dashed aromatic circle to a proper circle

[Norbert S. <st...@bb...>]

I think you can only show delocalized bonds as the additional dashed 
lines. It is not possible to show a circle.

Am 06.10.2023 um 08:56 schrieb Andrea Smith:
> https://pymolwiki.org/index.php/Valence
>
>
>
> On Thursday, October 05, 2023 17:56 CEST, Danilo Boskovic 
> <dan...@gm...> wrote:
>> Hey everyone,
>> Is it possible to change the dashed representation of aromatic circle 
>> to a proper circle?
>> If so, which commands should i use?
>> Thanks in advance!
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

-- 
-----------------------------------------------------------------------------
Norbert Straeter                                      fon +49 (0)341-97-31311
Univ.-Prof. Dr. rer. nat.
Center for Biotechnology and Biomedicine
Institute of Bioanalytical Chemistry
Faculty of Chemistry and Mineralogy
Leipzig University
Deutscher Platz 5
04103 Leipzig, Germany                             st...@bb...
  
https://www.bbz.uni-leipzig.de/en/research/structural-analysis-of-biopolymers
-----------------------------------------------------------------------------

Re: [PyMOL] Changing dashed aromatic circle to a proper circle

[Andrea S. <and...@uo...>]

https://pymolwiki.org/index.php/Valence



On Thursday, October 05, 2023 17:56 CEST, Danilo Boskovic <dan...@gm...> wrote:
 Hey everyone,
 Is it possible to change the dashed representation of aromatic circle to a proper circle?
 If so, which commands should i use?
 Thanks in advance!

[PyMOL] Changing dashed aromatic circle to a proper circle

[Danilo B. <dan...@gm...>]

Hey everyone,

Is it possible to change the dashed representation of aromatic circle to a
proper circle?

If so, which commands should i use?

Thanks in advance!

Re: [PyMOL] help with PyMOL rename command

[Norbert S. <st...@bb...>]

Dear wdela,

usually each atom in a residue has a different atom name. If this is not 
the case, the rename command will rename the atoms, that do not have 
unique names within a residue. It appears as if you cannot specify which 
atom names the renamed atoms will get. If you want to change to specific 
atom names, use a text editor.

Say ligand.pdb contains a molecule with some identically named atoms.

load ligand.pdb, ligand
rename ligand

This will automatically rename atoms to ensure unique atom names.

select mysel, ligand and name CA
rename mysel

Will only rename atoms CA to ensure unique atoms names.

You can apply the command to objects or selections.

Best wishes,

Norbert


Am 01.10.2023 um 17:28 schrieb wdela--- via PyMOL-users:

> Hi need help with PyMOL rename command:
>
> from https://pymolwiki.org/index.php/Rename :
>
>
>   Rename
>
> *rename* creates new atom names which are unique within residues.
>
>
>       USAGE
>
>
>         CURRENT
>
> rename  object-name  [  ,force  ]
> force  =  0  or  1  (default:  0)
>
>
>         PROPOSED
>
> rename  object-or-selection,force
>
>
>       NOTES
>
> To regerate only some atom names in a molecule, first clear them with 
> an "alter (sele),name=/“ commmand, then use "rename”/
> ........................................................................................... 
>
> Does 'rename test' create 'test' atom name ?? If so how do I apply it 
> to a selection ? I know how to use set_name to change an 
> object/selection name : https://pymolwiki.org/index.php/Set_name or 
> alter to change a property over a selection : 
> https://pymolwiki.org/index.php?title=Alter&redirect=no Cannot figure 
> out how rename works
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] help with PyMOL rename command

[<wd...@li...>]

Hi need help with PyMOL rename command:

 

from https://pymolwiki.org/index.php/Rename :


Rename

 
rename creates new atom names which are unique within residues.
 


USAGE


CURRENT

rename object-name [ ,force ]
force = 0 or 1 (default: 0)


PROPOSED

rename object-or-selection,force



NOTES

To regerate only some atom names in a molecule, first clear them with an "alter (sele),name=“ commmand, then use "rename”
...........................................................................................



Does 'rename test' create 'test' atom name ??

If so how do I apply it to a selection ?

I know how to use set_name to change an object/selection name : https://pymolwiki.org/index.php/Set_name

or alter to change a property over a selection : https://pymolwiki.org/index.php?title=Alter&redirect=no


Cannot figure out how rename works 


 

 

[PyMOL] H-bond data extraction

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

This is not a question related to PyMOL, but I was wondering if someone can
help me or guide me to the appropriate resource.

I extracted two types of H-bond occupancy data (donor: Lysine side chain
and backbone amide NH, with backbone carbonyl CO as acceptor) from two
different trajectories of the same peptide, centroid structures from
predominant cluster of each trajectory shown in each row. These structures
just differ by dihedral angles across a few residues.

Question: What is the best way to quantify relative strength of total
intramolecular hydrogen bonding between these two trajectories?
[image: image.png]
Many thanks,
Neena
Graduate student, U of T

[PyMOL] Problem with opening PDB file in pymol

[Kamlesh K. <kam...@gm...>]

Dear pymol users

I am opening a PDB file in pymol but it seems it has some problem in its
definition file.
Here I am attaching an image for reference. Please guide me on how to fix
this problem.

Thank you

[image: image.png]

Re: [PyMOL] Educational license download email not received

[Bennett,Antonette D <de...@uf...>]

Good morning, Alice I had the same problem, and it is still not resolved. Hopefully, you will get a better answer than I did (which is - you will receive it by email).

Antonette Bennett (PhD)
University of Florida
Dept. of Biochemistry and Molecular Biology
Center for Structural Biology
The McKnight Brain Institute
P.O. Box 100245,
Gainesville, FL 32610
University of Florida Lab Tel: 1-352-294-8394
Email:de...@uf...
________________________________
From: Alice Robson <a.r...@br...>
Sent: Tuesday, September 19, 2023 5:02 AM
To: pym...@li... <pym...@li...>
Subject: [PyMOL] Educational license download email not received

[External Email]
My students and I are trying to register for the educational build of Pymol, however, when we complete the online form we aren't receiving the email with the license. We've tried checking junk folders. Can anyone advise?

Many thanks,
Alice Robson
University of Bristol

[PyMOL] Educational license download email not received

[Alice R. <a.r...@br...>]

My students and I are trying to register for the educational build of Pymol, however, when we complete the online form we aren't receiving the email with the license. We've tried checking junk folders. Can anyone advise?

Many thanks,
Alice Robson
University of Bristol