pymol-users — Collaborative support and tips for PyMOL users

[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

[PyMOL] Mutagenesis on apo structure and/or complex with adduct atoms removed?

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

A single residue change in the enzyme active site confers resistant to inhibitor (adduct). Structures of apo enzyme and complexed with adduct available. Should I do the mutagenesis on the apo or on the complex after removal of the adduct atoms and relaxing the structure? When I align the apo structure with the complex or the adduct-removed structure the RMSD values are 0.47 and 0.52, respectively.

Re: [PyMOL] Extract relative helical character

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

Thank you all for your help,

I am sorry for not framing my question clearly. So I want to learn
what percentage of residues are helical in each peptide structure (is this
possible on PyMOL?); then I can compute the difference in helical content %
between both structures.

Many thanks,
Neena

On Sun, 11 Sept 2022 at 09:15, Thomas Holder <th...@th...>
wrote:

> Hi Neena,
>
> Not sure if I understand your question correctly, but if you are looking
> for the number of helix residues or the relative helix content, you can do
> this:
>
> count_helix = cmd.count_atoms("guide & ss H")
> count_all = cmd.count_atoms("guide")
> print("Number of helix residues:", count_helix)
> print("Relative helix content:", count_helix / count_all)
>
> Cheers,
>
> Thomas
>
>
>
> On Sat, Sep 10, 2022 at 1:37 PM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hello PyMOL users,
>>
>> Could I please get some insights on this?
>>
>> Thank you,
>> Neena
>>
>> On Wed, 7 Sept 2022 at 12:06, Neena Susan Eappen <nee...@gm...>
>> wrote:
>>
>>> Hello PyMOL users,
>>>
>>> I was wondering how to extract the total extent of helicity between two
>>> peptide structures on Pymol.
>>>
>>>
>>> [image: image.png]
>>> [image: image.png]
>>> Any insight would be appreciated.
>>>
>>> Many thanks,
>>> Neena
>>>
>>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Extract relative helical character

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

Hi Neena,

Not sure if I understand your question correctly, but if you are looking
for the number of helix residues or the relative helix content, you can do
this:

count_helix = cmd.count_atoms("guide & ss H")
count_all = cmd.count_atoms("guide")
print("Number of helix residues:", count_helix)
print("Relative helix content:", count_helix / count_all)

Cheers,

Thomas



On Sat, Sep 10, 2022 at 1:37 PM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> Could I please get some insights on this?
>
> Thank you,
> Neena
>
> On Wed, 7 Sept 2022 at 12:06, Neena Susan Eappen <nee...@gm...>
> wrote:
>
>> Hello PyMOL users,
>>
>> I was wondering how to extract the total extent of helicity between two
>> peptide structures on Pymol.
>>
>>
>> [image: image.png]
>> [image: image.png]
>> Any insight would be appreciated.
>>
>> Many thanks,
>> Neena
>>
>> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Extract relative helical character

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

Hello PyMOL users,

Could I please get some insights on this?

Thank you,
Neena

On Wed, 7 Sept 2022 at 12:06, Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> I was wondering how to extract the total extent of helicity between two
> peptide structures on Pymol.
>
>
> [image: image.png]
> [image: image.png]
> Any insight would be appreciated.
>
> Many thanks,
> Neena
>
>

Re: [PyMOL] Solid stick between two residues?

[Kelvin B. L. <Kel...@ug...>]

  1.  Are you sure it is a bond and not merely a rendering artifact with two hydrogens superimposed on each other?  Have you tried flipping through rotamers for either side chain to see if this resolves the clash?


  1.  If it is a "real" bond intended by those who created the model, then there may be information describing it in the pdb header.


  1.  You can submit your pdb to molprobity.  It will give a list of contacts and clashes:  http://molprobity.biochem.duke.edu/

________________________________
From: Joel Tyndall <joe...@ot...>
Sent: Tuesday, September 6, 2022 21:09
To: Timofey Tyugashev <tyu...@ni...>; pym...@li... <pym...@li...>
Subject: Re: [PyMOL] Solid stick between two residues?

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


I agree with Tim, PyMOL simply adds bonds based on the geometry of the structure. The salt bridge is very close. The "problem" (if any) lies with the crystal structure coordinates

-----Original Message-----
From: Timofey Tyugashev <tyu...@ni...>
Sent: Tuesday, 6 September 2022 3:17 PM
To: pym...@li...
Subject: Re: [PyMOL] Solid stick between two residues?


> Dear pymol users,
> does anybody recognize this type of bond and can explain me what this is? It appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but for some reason PyMol connects the two amino acids with a stick?
>
> Kind regards,
> Matthias
>
PyMOL generally draws covalent bonds based on geometric distances between atoms. Probably in this case the salt bridge between two residues was tight enough for the software to mislabel it.


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Re: [PyMOL] Solid stick between two residues?

[Florian N. <mai...@na...>]

> On 5 Sep 2022, at 16:39, Bruhn, Matthias <mat...@tw...> wrote:
> 
> Dear pymol users,
> does anybody recognize this type of bond and can explain me what this is? It appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but for some reason PyMol connects the two amino acids with a stick?

Pymol will create a bond if the distance between the hydrogen of this lysine and the aspartate is too short.
I guess that the protonation of this protein was not properly done. 

Florian
 

[PyMOL] Extract relative helical character

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

Hello PyMOL users,

I was wondering how to extract the total extent of helicity between two
peptide structures on Pymol.


[image: image.png]
[image: image.png]
Any insight would be appreciated.

Many thanks,
Neena

Re: [PyMOL] Solid stick between two residues?

[Joel T. <joe...@ot...>]

I agree with Tim, PyMOL simply adds bonds based on the geometry of the structure. The salt bridge is very close. The "problem" (if any) lies with the crystal structure coordinates

-----Original Message-----
From: Timofey Tyugashev <tyu...@ni...> 
Sent: Tuesday, 6 September 2022 3:17 PM
To: pym...@li...
Subject: Re: [PyMOL] Solid stick between two residues?


> Dear pymol users,
> does anybody recognize this type of bond and can explain me what this is? It appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but for some reason PyMol connects the two amino acids with a stick?
>
> Kind regards,
> Matthias
>
PyMOL generally draws covalent bonds based on geometric distances between atoms. Probably in this case the salt bridge between two residues was tight enough for the software to mislabel it.


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Re: [PyMOL] Solid stick between two residues?

[Timofey T. <tyu...@ni...>]

> Dear pymol users,
> does anybody recognize this type of bond and can explain me what this is? It appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but for some reason PyMol connects the two amino acids with a stick?
>
> Kind regards,
> Matthias
>
PyMOL generally draws covalent bonds based on geometric distances 
between atoms. Probably in this case the salt bridge between two 
residues was tight enough for the software to mislabel it.

Re: [PyMOL] Solid stick between two residues?

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

One possibility is that it could be a duplicated hydrogen atom where each
has connectivity to either residue. I can't say for sure without seeing the
original file.

Best,
Jarrett J

On Mon, Sep 5, 2022 at 11:37 AM Bruhn, Matthias <mat...@tw...>
wrote:

> Dear pymol users,
>
> does anybody recognize this type of bond and can explain me what this is?
> It appears between a Lysine and an Aspartic acid. I expect a hydrogen bond,
> but for some reason PyMol connects the two amino acids with a stick?
>
>
>
> Kind regards,
>
> Matthias
>
>
>
>
>
> ------------------------------
>
> TWINCORE GmbH I Feodor-Lynen-Str. 7 I 30625 Hannover I
> https://www.twincore.de
>
> Geschäftsführer: Prof. Dr. Ulrich Kalinke
> Aufsichtsratsvorsitzender: Prof. Dr. med. Michael P. Manns
> HRB 203373, Amtsgericht Hannover
>
> Hinweise zur Erfüllung unserer Informationspflichten zur Verarbeitung
> personenbezogener Daten gemäß Art. 13, 14 DSGVO finden Sie unter:
> https://www.twincore.de/datenschutz/
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
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>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Solid stick between two residues?

[Bruhn, M. <mat...@tw...>]

Dear pymol users,
does anybody recognize this type of bond and can explain me what this is? It appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but for some reason PyMol connects the two amino acids with a stick?

Kind regards,
Matthias



________________________________

TWINCORE GmbH I Feodor-Lynen-Str. 7 I 30625 Hannover I https://www.twincore.de

Geschäftsführer: Prof. Dr. Ulrich Kalinke
Aufsichtsratsvorsitzender: Prof. Dr. med. Michael P. Manns
HRB 203373, Amtsgericht Hannover

Hinweise zur Erfüllung unserer Informationspflichten zur Verarbeitung personenbezogener Daten gemäß Art. 13, 14 DSGVO finden Sie unter: https://www.twincore.de/datenschutz/

[PyMOL] Fwd: PyMol Educational licence

[Simone D'A. <sim...@le...>]

---------- Forwarded message ---------
Da: Simone D'Alì <sim...@le...>
Date: gio 1 set 2022 alle ore 09:23
Subject: PyMol Educational licence
To: <he...@sc...>


Hi,
I'm a High School Teacher from "Centro Scolastico Leonardo da Vinci" of
Bergamo, Italy. I make a request of pymol education and i wait 36 hours, I
haven't any mails (included spam). I would like teach to my students to use
pymol tu study the proteic folding, I hope that you are able to help me.
Sincerely.
Prof S. D'Alì

-- 
Vi comunichiamo che sono stati effettuati tutti i possibili controlli per 
verificare che i file allegati, qualora ci fossero, siano esenti da virus. 
In ogni caso si declina ogni responsabilità in ordine alla trasmissione 
delle e-mail. *Avvertenze ai sensi della D.Lgs. 30/06/2003 n. 196.* Le 
informazioni contenute in questo messaggio di posta elettronica e/o nel/i 
file/s allegato/i, sono da considerarsi strettamente riservate. Il loro 
utilizzo è consentito esclusivamente al destinatario del messaggio, per le 
finalità indicate nel messaggio stesso. Qualora riceveste questo messaggio 
senza esserne il destinatario, Vi preghiamo cortesemente di darcene notizia 
via e-mail e di procedere alla distruzione del messaggio stesso, 
cancellandolo dal Vostro sistema. Costituisce comportamento contrario ai 
principi dettati dal D.Lgs. 196/2003 il trattenere il messaggio stesso, 
divulgarlo anche in parte, distribuirlo ad altri soggetti, copiarlo, od 
utilizzarlo per finalità diverse.

[PyMOL] fetch command no longer working

[Dale P. <dal...@gm...>]

Hi all,

The 'fetch' command in Pymol no longer works for me, with PyMol issuing a rather non-descript error message which I have attached here. Can anybody please help getting this working again?

I am currently using v2.5 of PyMol installed using the homebrew package manager.

Thanks!

Dale.

[PyMOL] Unable to use NVIDIA as GL_Vendor

[PALLAV S. <s.p...@ii...>]

Dear users,
I have been using PyMOL quite some time and the NVIDIA cannot be used for rendering although I have all the required drivers installed yet during the startup, I have been encountering a message like this:

PyMOL(TM) Molecular Graphics System, Version 2.3.0.
Detected OpenGL version 3.1. Shaders available.
 Geometry shaders not available
 Detected GLSL version 1.40.
 OpenGL graphics engine:
  GL_VENDOR:   Mesa/X.org
  GL_RENDERER: llvmpipe (LLVM 12.0.0, 256 bits)
  GL_VERSION:  3.1 Mesa 21.2.6
 Detected 16 CPU cores.  Enabled multithreaded rendering.

This is the information of my graphics card:
*-display
       description: VGA compatible controller
       product: GP104GL [Quadro P4000]
       vendor: NVIDIA Corporation
       physical id: 0
       bus info: pci@0000:65:00.0
       version: a1
       width: 64 bits
       clock: 33MHz
       capabilities: pm msi pciexpress vga_controller bus_master cap_list rom
       configuration: driver=nvidia latency=0
       resources: irq:48 memory:d7000000-d7ffffff memory:c0000000-cfffffff memory:d0000000-d1ffffff ioport:b000(size=128) memory:c0000-dffff

This means that the PyMOL is unable to use NVIDIA as the GL_Vendor and also the Quadro P4000 as the GL_RENDERER. Is there any way during installation by which I can utilize the NVIDIA graphics acceleration such that I get better performance during rendering?

Pallav Sengupta,
Research Scholar,
Computational Biology Lab,
Department of Bioscience and Bioengineering(BSBE),
Indian Institute of Technology, Guwahati.
Guwahati, 781039.

[PyMOL] View of the ligand binding site

[Enrico M. <jms...@gm...>]

Dear Pymol users
I am looking for a possibility to automatize orientation of the camera
on the ligand binding cavity working with different protein-ligand
complexes. Is it possible to calculate centroid of the ligand and then
orient the view of it ?
Many thanks in advance
Cheers,
Enrico

Re: [PyMOL] pymol for educational purpose

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

Hello,

Our mailing server issue was fixed yesterday. Please re-register and/or
check spam folders if it doesn't arrive. Otherwise, contact
he...@sc...

Best,

Jarrett J

On Fri, Jul 22, 2022 at 6:41 AM LETIZIA PIZZORNI <
let...@un...> wrote:

> Goodmorning,
> I am a student of the University of Pavia and i need pymol; I tried to
> register on the site for getting it free but the confirmation email didn't
> arrive. How can i fix this?
>
> Have a good day.
> Letizia Pizzorni.
> _______________________________________________
> 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] pymol for educational purpose

[LETIZIA P. <let...@un...>]

Goodmorning,
I am a student of the University of Pavia and i need pymol; I tried to
register on the site for getting it free but the confirmation email didn't
arrive. How can i fix this?

Have a good day.
Letizia Pizzorni.

Re: [PyMOL] Object name for each object in grid display mode

[Tomas M. <tom...@gm...>]

Hi Rintarou,

Your script works beautifully! Thanks a lot.

Best wishes,
Tomas

On Wed, Jul 20, 2022 at 3:50 AM Suzuki, Rintarou <rs...@af...> wrote:
>
> Hi Tomas,
>
> You can do it with the following script
>
>
> from pymol import cmd
>
> cmd.set('grid_mode', 1)
> ids = ("1A70", "1AG6", "1B9W", "1BJA", "1BM8", "1BMG", "1BOX", "1BTE",
> "1BXU", "1BXV", "1BYO", "1BYP")
>
> for i in ids:
>   cmd.fetch(i)
>   if i != "1A70":
>     cmd.cealign("1A70", i+" & c. A")
> cmd.zoom("all", "-20")
>
> for i in ids:
>   cmd.pseudoatom(i+"_info")
>   cmd.label(i+"_info", '"{}"'.format(i))
>   cmd.set('label_size', 16, i+"_info")
>   cmd.set('label_position', '0, 7, 10', i+"_info")
>   cmd.group(i+"_group", "{0} {0}_info".format(i))
>
> cmd.hide("everything", "r. hoh")
> cmd.hide("everything", "c. B")
> cmd.hide("nonbonded")
>
>
> Regards,
> Rintaro
>
>
> On 2022/07/20 1:48, Tomas Malinauskas wrote:
> > Dear All,
> >
> > Is it possible to show the object name for each object in grid display
> > mode? E.g. I have 12 PDBs loaded in grid mode and would like to show
> > their IDs (not in the side panel but in the main window) at the same
> > time.
> >
> > I thank you for your help.
> >
> > Best wishes,
> > Tomas
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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Re: [PyMOL] Object name for each object in grid display mode

[Suzuki, R. <rs...@af...>]

Hi Tomas,

You can do it with the following script


from pymol import cmd

cmd.set('grid_mode', 1)
ids = ("1A70", "1AG6", "1B9W", "1BJA", "1BM8", "1BMG", "1BOX", "1BTE",
"1BXU", "1BXV", "1BYO", "1BYP")

for i in ids:
  cmd.fetch(i)
  if i != "1A70":
    cmd.cealign("1A70", i+" & c. A")
cmd.zoom("all", "-20")

for i in ids:
  cmd.pseudoatom(i+"_info")
  cmd.label(i+"_info", '"{}"'.format(i))
  cmd.set('label_size', 16, i+"_info")
  cmd.set('label_position', '0, 7, 10', i+"_info")
  cmd.group(i+"_group", "{0} {0}_info".format(i))

cmd.hide("everything", "r. hoh")
cmd.hide("everything", "c. B")
cmd.hide("nonbonded")


Regards,
Rintaro


On 2022/07/20 1:48, Tomas Malinauskas wrote:
> Dear All,
> 
> Is it possible to show the object name for each object in grid display
> mode? E.g. I have 12 PDBs loaded in grid mode and would like to show
> their IDs (not in the side panel but in the main window) at the same
> time.
> 
> I thank you for your help.
> 
> Best wishes,
> Tomas
> 
> 
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[PyMOL] Object name for each object in grid display mode

[Tomas M. <tom...@gm...>]

Dear All,

Is it possible to show the object name for each object in grid display
mode? E.g. I have 12 PDBs loaded in grid mode and would like to show
their IDs (not in the side panel but in the main window) at the same
time.

I thank you for your help.

Best wishes,
Tomas