pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

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

Hi ZHANG Cheng,

Did you try?

set all_states, on;spectrum b

Another approach would to split the states into separate objects and then apply the 
spectrum command to each object. 

split_states protein.pdb; prefix=test;spectrum b,,test*

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: ZHANG Cheng [272...@qq...]
Sent: Sunday, August 30, 2020 4:40 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns.

After running the "spectrum b" command, the colouring is only based on the last state of the object.

So can I colour the frames differently using their corresponding b-factor values? In that case, I can see the colour changing throughout the frame playing.

Re: [PyMOL] [EXTERNAL] To remove non protein moiety

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

Hi Aswini,

Enter at the PyMOL prompt below the command history window the following command:

remove not polymer

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Ashwini S [ash...@gm...]
Sent: Monday, August 31, 2020 3:29 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] To remove non protein moiety

Hello, I am unable to remove non protein moiety. Is it possible?
If so please share the procedure.

Regards
Ashwini  s

[PyMOL] To remove non protein moiety

[Ashwini S <ash...@gm...>]

Hello, I am unable to remove non protein moiety. Is it possible?

If so please share the procedure.



Regards

Ashwini  s

[PyMOL] How to color based on b-factor for all the frames in one object in Pymol?

[<272...@qq...>]

I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns.

After running the "spectrum b" command, the colouring is only based on the last state of the object.


So can I colour the frames differently using their corresponding b-factor values? In that case, I can see the colour changing throughout the frame playing.

Re: [PyMOL] [EXTERNAL] How to select s series of residues that contain the selected atom

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

Hi Yeping,

You might try using the your atoms selection as input to the script listed here

https://pymolwiki.org/index.php/ListSelection2


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: sunyeping via PyMOL-users [pym...@li...]
Sent: Sunday, August 23, 2020 10:34 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to select s series of residues that contain the selected atom

Dear pymol user,

I select a series of atoms with the follow command in pymol:
    select atoms, chian A within 4 of chain B

I wonder how to select the resides containing the selected "atoms", and how to return the names and indexes of these residues.
Thank you in advance!

Best regards,
Yeping Sun

[PyMOL] How to select s series of residues that contain the selected atom

[sunyeping <sun...@al...>]

Dear pymol user,

I select a series of atoms with the follow command in pymol:
    select atoms, chian A within 4 of chain B

I wonder how to select the resides containing the selected "atoms", and how to return the names and indexes of these residues.
Thank you in advance!

Best regards,
Yeping Sun

Re: [PyMOL] [EXTERNAL] B-factor coloring scale

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

Hi Neena,

The default palette for coloring the B-factor is the rainbow palette:

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

You can control the range of B-factors to which the scale is applied with the spectrum command:

spectrum b, rainbow, minimum=10, maximum=50

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Neena Susan Eappen [nee...@gm...]
Sent: Saturday, August 22, 2020 1:35 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL]  B-factor coloring scale

Hello PyMOL users,

Where can I find the coloring scale used for B-factor in PyMOL?

Many thanks,
Neena

[PyMOL] B-factor coloring scale

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

Hello PyMOL users,

Where can I find the coloring scale used for B-factor in PyMOL?

Many thanks,
Neena

[PyMOL] May I hire you to assist me

[Chris M. <dr....@ya...>]

Hello   I wish to hire someone to assist me with the demonstration of active sites and molecular structure and function. A knowledge of the use of  PDB is also helpful. my email is dr....@ya...  

[PyMOL] volume calculation

[Yang S. <ysh...@gm...>]

Dear PYMOL developer(s),
Is there a way to calculate the volume of a U-shaped groove which is formed by the side chains of two adjacent residues.
Thanks in advance,
Yang

[PyMOL] Issues with Python API when saving images inside a loop

[Antonio S. <ase...@uc...>]

I have a Python script that constantly saves images from a given unique
session inside a triple loop through the API command "png":

for i_episode in range(len(num_episodes)):
    for i_step in range(len(num_steps)):
        for i_views in range(len(num_views)):
            sess.cmd.png("./position_" + str(i_views), width=84, height=84,
dpi=-1.0, ray=0, quiet=1)

The session is always the same and I never close it during the execution of
the entire program. The problem is that it does not generate the images
correctly. In addition, this wrong behavior seems random up to a certain
extent. That is, sometimes the execution freezes when it arrives at the
aforementioned line of sess.cmd.png... Sometimes, the loop generates the
images correctly for certain episodes but for others these are blank (in
those cases, the files are generated but their size is only 169 bytes when
it should have around 3 Kb).

Is there any feature about PyMol sessions and/or png files generation that
I should know beforehand when using the Python API of PyMol? Any clue to
solve this issue?

Many thx,
Antonio Serrano

-- 

"Este mensaje es privado y confidencial y se dirige exclusivamente a su 
destinatario. Si usted recibe este mensaje por error, no debe revelar, 
distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y 
borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a 
la confidencialidad ni a ningún privilegio a causa de una transmisión 
errónea o por mal funcionamiento". 


"This message is private and 
confidential and it is intended exclusively for the addressee. If your 
receive this message by mistake, you should not disseminate, distribute or 
copy this e-mail. Please inform the sender and delete the message and 
attachments from your system. No confidentiality or any privilege regarding 
the information is waived or lost by any mistransmission or malfunction".



No me imprimas si no es necesario.Don't print me unless it's necessary.

[PyMOL] Drawing box around active site

[Jatin K. <jk...@nj...>]

Hi, 

I am new to PyMol. I have coordinates and size of a box around active site in a protein.
I want to do the visual inspection of the protein. Can I do that in PyMol. 
Can anybody please provide relative tutorial.

Thank you.



——
Jatin 

NJIT, Newark
NJ

Re: [PyMOL] Command varargs

[Thomas H. <tho...@sc...>]

Hi Pedro,

Add `_self=pymol.cmd` as a keyword argument, then it should work
properly as a command.

@pm.extend
def func(*args, kw1=1, kw2=True, _self=pm):
  pass

Cheers,
  Thomas

On Thu, Jul 30, 2020 at 11:52 AM Pedro Lacerda <psl...@gm...> wrote:
>
> Hi,
>
> How can I accept variable arguments in my command? My first attempt was:
>
> @pm.extend
> def func(*args, kw1=1, kw2=True):
>   pass
>
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Command varargs

[Pedro L. <psl...@gm...>]

Hi,

How can I accept variable arguments in my command? My first attempt was:

@pm.extend
def func(*args, kw1=1, kw2=True):
  pass


-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] transform an channel pore profile

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

I got the answer.

Actually, the solution is so simple, matrix_copy.

Charles
________________________________
From: Chen, Qiang
Sent: Friday, July 24, 2020 12:46 PM
To: pym...@li... <pym...@li...>
Subject: transform an channel pore profile

Hi, Pymol users,

Would anyone help me to transform the calculated pore profile along with the protein.

I have a couple of proteins and I calculated the pore profiles using MOLE. I downloaded the pymol scripts to regenerate the pores with the protein. when I aligned these proteins, the pore apparently won't be aligned.

One solution is aligning all the proteins and then calculating the pore profiles. The issue is anytime I have a new protein, I need align it first and then calculate the pore profile.

Would there be a better way in this scenario if I already have the pore profiles?

I guess object_matrix can do this.

Then the question is how can I get the transformation matrix from align/super/cealign, and then transform the pore profile.

All recommendations and suggestions are welcome! Appreciating your help!

Thanks,
Charles

[PyMOL] How to do a summary distance?

[Полина К. <kor...@gm...>]

Hello, everyone! I want to make a summary distance: I want to summarise measurements of distances, for example dist1 = 8.2, dist2 = 9.1 and I want PyMOL to write somewhere dist1+dist2 = 8.2+9.1 = 17.3. Is it possible? 

Thank you, Polina. 

[PyMOL] transform an channel pore profile

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

Hi, Pymol users,

Would anyone help me to transform the calculated pore profile along with the protein.

I have a couple of proteins and I calculated the pore profiles using MOLE. I downloaded the pymol scripts to regenerate the pores with the protein. when I aligned these proteins, the pore apparently won't be aligned.

One solution is aligning all the proteins and then calculating the pore profiles. The issue is anytime I have a new protein, I need align it first and then calculate the pore profile.

Would there be a better way in this scenario if I already have the pore profiles?

I guess object_matrix can do this.

Then the question is how can I get the transformation matrix from align/super/cealign, and then transform the pore profile.

All recommendations and suggestions are welcome! Appreciating your help!

Thanks,
Charles

[PyMOL] How to make a distance when atoms cross the cell and appear on the other side?

[Полина К. <kor...@gm...>]

Hello, everybody. I want to connect and measure a distance between atoms but some of them flew away across cell borders. What should I do?

Best wishes,
Korotkova Polina. 

Re: [PyMOL] Remove/keep every n_th (dummy) atom of a selection

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

Hi Fred,

You can select the dummy atoms to keep via the id identifier by entering the following command at the PyMOL prompt:

select keep, id 1 or id 6 or id 12 or id 18 or id 24 


Then you could remove the dummy atoms outside of the selection by entering the following command at the PyMOL prompt:

remove not keep


To count the number of dummy atoms, you can enter the following command at the PyMOL prompt:

count_atoms

Say you have 6000 dummy atoms, making the above selection by hand will be tedious.
You can enter Python code at the PyMOL prompt to generate the selection.
Enter the following command to make a list of every 6th integer.

kid = [x * 6 for x in range(1000)]

Now unpack the list called 'kid' onto one line with the required format.
It is critical that retain the whitespaces in ' or id '.

print(*kid, sep=' or id ')

Replace the "0 " at the first entry with "id 1 ".
Now use this expression to create the selection called "keep" in the first command above.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: belzebub [bel...@gm...]
Sent: Wednesday, July 22, 2020 4:36 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Remove/keep every n_th (dummy) atom of a selection

Hi guys,

I'm quite new to Pymol and facing some hurdle that costs a lot of time.
Maybe someone of you knows a quick solution.

I have a selection (sele) of dummy atoms and need to reduce the number
of these atoms to about 15-20. To be more precise, I want to

- keep 1 atom
- remove e.g. the next 5 atoms
- keep 1 atom
- remove e.g. the next 5 atoms
- and so on

Is there an easy way to accomplish that directly on the Pymol command line?

Many thanks in advance!

Fred




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Re: [PyMOL] Remove/keep every n_th (dummy) atom of a selection

[belzebub <bel...@gm...>]

Sorry, a little mistake: want to reduce the number of atoms to about 15-20% ...

Am 22.07.20 um 11:36 schrieb belzebub:
> Hi guys,
>
> I'm quite new to Pymol and facing some hurdle that costs a lot of time.
> Maybe someone of you knows a quick solution.
>
> I have a selection (sele) of dummy atoms and need to reduce the number
> of these atoms to about 15-20. To be more precise, I want to
>
> - keep 1 atom
> - remove e.g. the next 5 atoms
> - keep 1 atom
> - remove e.g. the next 5 atoms
> - and so on
>
> Is there an easy way to accomplish that directly on the Pymol command line?
>
> Many thanks in advance!
>
> Fred
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Remove/keep every n_th (dummy) atom of a selection

[belzebub <bel...@gm...>]

Hi guys,

I'm quite new to Pymol and facing some hurdle that costs a lot of time.
Maybe someone of you knows a quick solution.

I have a selection (sele) of dummy atoms and need to reduce the number
of these atoms to about 15-20. To be more precise, I want to

- keep 1 atom
- remove e.g. the next 5 atoms
- keep 1 atom
- remove e.g. the next 5 atoms
- and so on

Is there an easy way to accomplish that directly on the Pymol command line?

Many thanks in advance!

Fred

[PyMOL] Pymol course

[Rana H. <hus...@gm...>]

Hi All,

I am preparing a simple intro for pymol for my students at my university
and I am wondering if its fine to copy some part and take pics from the
pymol manual and the wiki. Or I have to paraphrase first and ask first for
the copyright permission.
Again it is only for educational purposes in the university.

Best regards



-- 
  Rana Hussein Ali
Graduate Research Assistant
Humboldt-Universität zu Berlin
Institute of Biology
Philippstraße 13 (Haus 18)
10115 Berlin, Germany
Tel. +4930 - 2093-47933

Re: [PyMOL] User data

[Pedro L. <psl...@gm...>]

Hi,

I opted for

> This works on all platforms:
> os.path.expanduser("~/.pymol/myplugindata")
>

And it is working here:
https://github.com/pslacerda/pymol-labimm/blob/f8d4906f89c0cae3f6c5b504cc78a9bbf70565d1/pymol_labimm/prefs.py#L40


Em seg., 15 de jun. de 2020 às 05:08, Thomas Holder <
tho...@sc...> escreveu:

> Hi Pedro,
>
> There is no designated infrastructure for this. Other plugins typically
> create their own directory in the user's home folder, like
> "~/.myplugindata". You could also create it inside the "~/.pymol" directory
> (like "~/.pymol/myplugindata").
>
> This works on all platforms:
> os.path.expanduser("~/.pymol/myplugindata")
>
> On Windows, you could also put it inside the %APPDATA% directory:
> os.path.join(os.environ['APPDATA'], 'pymol', 'myplugindata')
>
>
> Let me know how you decide or if you have other ideas!
>
> Cheers,
>   Thomas
>
>
> > On Jun 9, 2020, at 10:20 PM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > Hi PyMOL users and developers,
> >
> > I have a plugin that needs to download data periodically. Where should I
> download to?
> >
> > By the way, I managed to get a plugin into a python package.
> >
> >
> https://github.com/pslacerda/pymol-labimm/blob/master/scripts/pymol_labimm.py
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] Pymol Will Not Open PDBs on a New HDD

[Michael B. <mic...@sf...>]

Hi,


I recently moved my documents to a new hard drive disk. Interestingly, Pymol will not open any pdb's in the new location. When the same file was moved outside the new disk the problem goes away. Other visualization programs, e.g. Chimera, work fine. I'm working on Ubunut 20.04, and I'm using Pymol 2.41. The error I get is not specific:



Error: failed to open file "/folder_directory/name.pdb
Error: Argument processing aborted due to exception (above).


Any ideas what's happening?


--Mike

Re: [PyMOL] Reading Cell Dimensions from GROMACS XTC file

[Thomas H. <tho...@sc...>]

Hi Dan,

Showing different cells for each state is currently not implemented, but I think it would not be too difficult to add support for that.

I've opened a feature request ticket:
https://github.com/schrodinger/pymol-open-source/issues/114

Cheers,
  Thomas


> On Jul 13, 2020, at 4:20 PM, Daniel Kozuch <dk...@pr...> wrote:
> 
> Hello,
> 
> I would like to load a GROMACS xtc trajectory and visualize the (changing) cell size.
> 
> My current workflow is:
> 
> load sim.pdb
> load_traj sim.xtc, sim
> show cell
> 
> This shows a cell/box but it is the wrong size and does not update every frame. Is there some way to load the proper cell dimensions?
> 
> Best regards,
> Dan Kozuch
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.