pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Get/edit molecule title?

[Petro <sub...@kh...>]

Hi, list.
When I load the mol2 file, the title of the molecule is shown near the
object name in green in the internal GUI. Is there a way to read it? Maybe
even edit it?
Thanks.
Petro.

[PyMOL] Bond Editing

[Jason W. <Jas...@ne...>]

Hi all,

This is a long shot. But I am having problems fitting a model to a cryoEM map with bond modifications completed in pymol and I am hoping someone can help.

I downloaded a structure from the PDB database, and I am adding two bonds between nucleotides. However, these bonds do not appear to save correctly to mmCIF or PDB, often being lost as they do not show up in ChimeraX. When trying to open these files again in pymol, I can see random things like a hydrogen with two bonds in place of the new bond I made. The modifications appear to save okay to mol2, but phenix refuses to use the file afterwards anyway.

I feel like I am missing a step because phenix asks for restraints and when I try to run elbow, it just crashes with the PDB and mmCIF files. The Mol2 file does not load in phenix and just crashes phenix. I have gotten the mol2 file to open in chimeraX and then save as pdb afterwards. I did generate restraints for this file, but it completed this without the actual modifications I made so was pointless.

So, I am kind of stumped right now. Has anyone had any experience with creating new bonds in PDB files and saving them for use with fitting to cryoEM maps and refinement?

Thanks,
Jason Woodgate
Newcastle University.

[PyMOL] Application

[<496...@qq...>]

I am a student. I applied for a free download voucher on the website, but I haven't sent an email to me. I hope you can reply as soon as possible. Thank you！！！

[PyMOL] Pymol registration Problem

[Islam, S. [GDCBS] <sa...@ia...>]

Hi,
I wanted to register using giving my credentials and email id to Pymol for educational purpose on 25th December. I did not get any registration confirmation email. I checked my inbox and Junk Folder on outlook. No email from Pymol. Then I emailed Pymol regarding the problem @he...@sc.... I still did not get a reply. Could you help?

---------------
Saiful Islam
Interdepartmental Plant Biology, Ph.D. Program
Graduate Research Assistant, Aung Lab
Dept. of Genetic, Development, and Cell Biology
Iowa State University
3339-7 ATRB, 2213 Pammel Dr,
Ames, IA 50011-4009

[PyMOL] Question regarding transparency

[wenchao z. <zha...@gm...>]

Dear Pymol users,

I have a question about transparency.

I would like to transparent both the cartoon and the surface to highlight
the sticks, but when I transparent both of them, the cartoon will
disappear, how do you solve this?

Thank you in advance!

[PyMOL] plotting atoms around aromatic side chain

[Yogesh S. <yog...@gm...>]

hi all,

I am trying to graph the  diversity of amino acids on both planes of the
aromatic side chain of tryptophan, but not getting any hint of where to
start. Is there any way to map 3D coordinates on a 2d plot?
Please suggest.
 *  with  regards*
*Yogesh Sharma*

[PyMOL] Cover images of the RNA Journal generated by the NDB using DSSR and PyMOL

[Xiang-Jun Lu <3d...@gm...>]

Dear list members,

I thought it is worth noting that the 2x12 cover images of the *RNA Journal*
in 2021 and 2022 have all been generated by the Nucleic Acid Database (
ndbserver.rutgers.edu) using DSSR and PyMOL. See the composite at
http://docs.x3dna.org/images/RNAcovers-NDB-dssr-pymol.png and the December
2022 issue at https://rnajournal.cshlp.org/content/28/12.cover-expansion

Users can easily generate such highly simplified, yet informative images of
nucleic acid structures using http://skmatic.x3dna.org

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

Re: [PyMOL] [EXTERNAL] Questions regarding selection

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

Hi Prathvi,

You will find answers to the first three questions on the PyMOL wiki: https://pymolwiki.org/index.php/Selection_Algebra

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________
From: Prathvi Singh <pr...@ii...>
Sent: Wednesday, November 23, 2022 1:16 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Questions regarding selection

Hi,

I have a few questions regarding selection command for which I am unable to find the answers:

How to select, say 100th and 120th residue of chain-A and 50th residue of chain-B?
How to select all the alanine residues of chain-A and glycine residues of chain-B?
How to count the total number of selected residues?
How to display residue information on hovering the mouse over it like in UCSF chimera?

Thanks in advance
--
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016

[PyMOL] Questions regarding selection

[Prathvi S. <pr...@ii...>]

Hi,

I have a few questions regarding selection command for which I am unable to
find the answers:

How to select, say 100th and 120th residue of chain-A and 50th residue of
chain-B?
How to select all the alanine residues of chain-A and glycine residues of
chain-B?
How to count the total number of selected residues?
How to display residue information on hovering the mouse over it like in
UCSF chimera?

Thanks in advance
-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016

Re: [PyMOL] Loading gromacs and amber trajectory

[Jarrett J. <jar...@sc...>]

Hello,

https://www.pymolwiki.org/index.php/Load_traj outlines the steps to load
gromacs (two steps: load gro structure file, then xtc trajectory files) and
other types of trajectory files into PyMOL.

Hope this helps,

Jarrett J.


On Fri, Nov 18, 2022 at 11:03 AM Khoroshyy Petro <kho...@gm...>
wrote:

> Hi.
> Is there a way to load gromacs and amber trajectory?
> Thanks
> Petro
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] High surface quality for large structures - hardware requirements

[Natalia <N.M...@hh...>]

Hello Pymol community!

I would like to be able to render high quality images of a surface representation of large structures, such as the ribosome. 
However when I set the surface quality to 2, on my machine it takes ages to get the surface representation.
Would a GPU be of any use to speed up this step, or is it used only in the rendering step?  Which would be the hardware requirements to speed this up and make it run more smoothly?

On our server (Linux) this process uses really little RAM and 1 thread, and after 2 hours it gives out the error message: CGO-Error: CGOCombineBeginEnd: invalid op=0x00 inside BEGIN/END
Does anyone know what it means?

I really wasn´t able to detect which hardware component is the bottleneck.
I would be very grateful if someone could help me out!

Cheers,

Natalia

[PyMOL] Loading gromacs and amber trajectory

[Khoroshyy P. <kho...@gm...>]

Hi.
Is there a way to load gromacs and amber trajectory?
Thanks
Petro

[PyMOL] mutagenesis - dashed yellow lines hide?

[Colin D. <Col...@uw...>]

During mutagenesis dashed yellow lines appear from the main chain of the new aa with distances attached and they remain when moving through the various rotamer states. Is there a way of hiding these lines and labels?

[PyMOL] Slab on external screen with open source PyMOL

[Marko H. <mh...@ca...>]

Hello PyMOLlers,

I have an annoying "feature" on my Win (2.5.0 Open source) PyMOL in that I cannot use scroll mouse to Z-slab the view on a second screen. A second laptop where I have the same, with external monitor connected either with UCB-C  or HDMI. Works ok if I move the PyMOL window back to laptop screen, but no action on the second screen. Shift-Right-Mouse for front/back clip works, as does command line eg. "clip slab, 10". Just not scroll wheel slab.

Anyone had the same and been able to fix it or suggestions on what to try?

Cheers, Marko
---------
Marko Hyvonen
Department of Biochemistry
University of Cambridge
mh...@ca...<mailto:mh...@ca...>
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup

Re: [PyMOL] STRIDE plugin for Pymol

[Chris F. <fa...@gm...>]

Hi Thomas,

Thanks for looking into it! Unfortunately, I don't currently have access to
a Linux system. These plugins don't seem to be compatible with Pymol on
Windows?

Best,
Chris

On Tue, Nov 1, 2022 at 8:35 PM Thomas Holder <th...@th...>
wrote:

> Hi Chris,
>
> The plugin works for me on Linux with PyMOL 2.5.2. I've installed
> stride from https://anaconda.org/ostrokach-forge/stride and the plugin
> with the plugin manager using the
> https://pymolwiki.org/index.php/DSSP_Stride URL.
>
> Cheers,
>   Thomas
>
> On Sat, Oct 29, 2022 at 4:29 PM Chris Fage <fa...@gm...> wrote:
> >
> > Dear All,
> >
> > Does anyone use the STRIDE plugin here with any version of Pymol?
> Installing it with the plugin manager in Pymol 1.3 or 2.3.1 doesn't seem to
> work for me. Unfortunately, the original STRIDE server seems to be
> inaccessible these days.
> >
> > Cheers,
> > Chris
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] hiding the main chain for a named selection?

[Marko H. <mh...@ca...>]

Hi Colin,

>From memory (and assuming no hydrogens)
hide everything, name C+N+O & yourselection

Marko

---------
Marko Hyvonen
Department of Biochemistry
University of Cambridge
mh...@ca...
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup


________________________________
From: Colin Dolphin via PyMOL-users <pym...@li...>
Sent: Wednesday, November 2, 2022 2:21:51 PM
To: pym...@li... <pym...@li...>
Subject: [PyMOL] hiding the main chain for a named selection?

Newbie here. Is there a way to script hiding the main chain for a named selection as per the GUI (H-main chain)?

[PyMOL] hiding the main chain for a named selection?

[Colin D. <Col...@uw...>]

Newbie here. Is there a way to script hiding the main chain for a named selection as per the GUI (H-main chain)?

Re: [PyMOL] STRIDE plugin for Pymol

[Thomas H. <th...@th...>]

Hi Chris,

The plugin works for me on Linux with PyMOL 2.5.2. I've installed
stride from https://anaconda.org/ostrokach-forge/stride and the plugin
with the plugin manager using the
https://pymolwiki.org/index.php/DSSP_Stride URL.

Cheers,
  Thomas

On Sat, Oct 29, 2022 at 4:29 PM Chris Fage <fa...@gm...> wrote:
>
> Dear All,
>
> Does anyone use the STRIDE plugin here with any version of Pymol? Installing it with the plugin manager in Pymol 1.3 or 2.3.1 doesn't seem to work for me. Unfortunately, the original STRIDE server seems to be inaccessible these days.
>
> Cheers,
> Chris
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Automatically change the pwd to the directory where I drag&dropped from?

[Yike <kal...@gm...>]

Dear Sir/Madam, I wish to cd into the directory which I drag&dropped a .pdb
file from in Pymol automatically upon drag&dropped such that I can run some
python script in the directory. But I don't know a way to do so.
For example, I want to pymol change the current working directory
automatically to the one where I drag&drops a .pdb file from.
Or is there any stored variable of the directory of the current object I
drag&dropped from?

Thanks
Best Regards
Rico

Re: [PyMOL] Gradient colouring

[Dheeraj P. <dh...@gm...>]

Hi Tanaya,

You can replace the default B-factor values in a PDB file with user defined
values.

Check out these links. They show how to use values from a user-defined file
and set a color gradient on your protein:
1. https://pymolwiki.org/index.php/Load_new_B-factors
2. https://pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring

Hope this helps. All the best.

Best regards,
-----------------------------------------------------
*Dr Dheeraj Prakaash*
Postdoctoral Research Associate
Syma Khalid Research Group <https://symakhalidresearchgroup.wordpress.com/>
Department of Biochemistry <https://www.bioch.ox.ac.uk/>
University of Oxford <https://www.ox.ac.uk/>

Web: LinkedIn <https://www.linkedin.com/in/dheeraj-prakaash-b757679a/> |
Twitter <https://twitter.com/DJ_Biophys> | ResearchGate
<https://www.researchgate.net/profile/Dheeraj-Prakaash>
-----------------------------------------------------

[PyMOL] STRIDE plugin for Pymol

[Chris F. <fa...@gm...>]

Dear All,

Does anyone use the STRIDE plugin here
<https://pymolwiki.org/index.php/DSSP_Stride> with any version of Pymol?
Installing it with the plugin manager in Pymol 1.3 or 2.3.1 doesn't seem to
work for me. Unfortunately, the original STRIDE server seems to be
inaccessible these days.

Cheers,
Chris

[PyMOL] Gradient colouring

[Tanaya B. R. B. R. <ta...@ii...>]

Hello everyone!

I am interested to know how to apply gradient colouring to the protein of my interest based on user-defined values (not b factor or RMSD). What should be the type and format of this user defined file, specifying the values? And what is the command for implementing this?

It would be really useful if you could guide me to do this.

Thank you,
Tanaya

[PyMOL] r, theta, and phi of a helix

[Chen, Q. <qi...@pi...>]

Hi, Pymol Users,

How can I extract the orientation of the helix region of a protein?

For example, I have a pentameric membrane protein, I would like to know the orientation angle of one helix region relative to the pentameric symmetry axis (Z)?

I found there is a script to calculate the angle between two helical regions.

Thanks!

Charles

[PyMOL] problem on generating vacuum electrostatics in PyMol 2.5.4

[<wi...@ga...>]

Hi,

 

I have just switched to the new PyMol version of 2.5.4, and am encountering
a problem while trying to generate the vacuum electrostatics for a protein.

However, I am getting an error message of 

"Pop-Error: invalid source selection name 'assign_tmp1'"

 

I have never encountered this sort of problem with earlier version of PyMol
before. 

 

Any advice will be appreciated.

 

Thanks,

 

Best wishes,

 

Winston

 

[PyMOL] 15th Annual CCP4/APS Crystallographic School (onsite)

[Qingping Xu <qx...@an...>]

Dear Colleagues,

We are pleased to announce the 15th annual CCP4/APS crystallographic 
school “From data collection to structure refinement and beyond” will be 
held on March 27th to April 3rd, 2023 at the Advanced Photon Source 
(APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. 
All details can be found at the school website: 
http://www.ccp4.ac.uk/schools/APS-2023/index.php. This will be our first 
post-COVID in person workshop, scheduled before the APS upgrade shutdown.


Dates: March 27 through April 3, 2023
Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near
Chicago), Illinois, USA

The school comprises two parts: data collection workshop and 
crystallographic computing workshop. Data collection workshop includes 
beamline training, data collection on GM/CA@APS beamlines 23ID-D and 
23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, 
and data processing. For data collection, only the participants' 
crystals will be used. Crystallographic computation workshop will 
feature many modern crystallographic software packages taught by authors 
and other experts. The daily schedule will be organized in three 
sections – lectures, tutorials, and hands-on (interactive 
trouble-shooting of the technical difficulties the participants face in 
their projects). We have had considerable success resolving these 
problems in past years, attested by resulting publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft 
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert 
help with difficulties/challenges in their own projects. Graduate 
students, postdoctoral researchers and early-career faculty, along with 
commercial/industrial researchers are encouraged to apply. Only about 20 
applicants will be selected for participation.

Application: Application deadline is Jan 31th, 2023. To apply, visit  
https://www.ccp4.ac.uk/schools/APS-2023/application.php

Fees: There is a $500 participation fee for the selected academic 
students and $1500 for industrial researchers. No credit card will be 
required for registration, students who are selected to participate will 
be contacted to pay. The students will be responsible for their 
transportation and lodging. The workshop organizers can assist in making 
lodging reservations at the Argonne Guest House. The workshop will cover 
all other expenses (including meals).


We hope to see you at the school.


Charles, Andrey, Garib and Qingping