pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] User data

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

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.

Re: [PyMOL] APBS plugin for Sugars

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

Hi Mario,

Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, the AMBER force field data files can be found like this:

$ find . -name "AMBER.*"
./lib/python3.7/site-packages/src/dat/AMBER.names
./lib/python3.7/site-packages/src/dat/AMBER.DAT


Hope that helps.

Cheers,
  Thomas


> On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena <ma...@cm...> wrote:
> 
> Hi all,
>  
> I was trying to generate dipole moments with pymol using the APBS plugin. For proteins I adapted a code and the dipole moments are correct and work just fine, but for sugars it does not. I am well aware that the problem is that many of the residues are not present in the AMBER force field data (or the force field I want to use.) In APBS it is relatively easy to adapt and introduce the sugars’ information manually, however in the APBS plugin for pymol gets a little bit thorny. I cannot seem to find the files where I should store the sugar information. Has anybody done this before? Any alternatives with other programs or approaches are also welcome.
>  
> Thank you in advance,
>  
> Mario
> _______________________________________________
> 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.

[PyMOL] APBS plugin for Sugars

[Mario G. U. <ma...@cm...>]

Hi all,

I was trying to generate dipole moments with pymol using the APBS plugin. For proteins I adapted a code and the dipole moments are correct and work just fine, but for sugars it does not. I am well aware that the problem is that many of the residues are not present in the AMBER force field data (or the force field I want to use.) In APBS it is relatively easy to adapt and introduce the sugars' information manually, however in the APBS plugin for pymol gets a little bit thorny. I cannot seem to find the files where I should store the sugar information. Has anybody done this before? Any alternatives with other programs or approaches are also welcome.

Thank you in advance,

Mario

Re: [PyMOL] PyMOL-users Digest, Vol 169, Issue 9

[Len B. <ban...@um...>]

> On Jun 7, 2020, at 17:28, pym...@li... wrote:
> 
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
> 
> You can reach the person managing the list at
> 	pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: View two proteins from one pdb file (Joel Tyndall)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 7 Jun 2020 22:28:14 +0000
> From: Joel Tyndall <joe...@ot...>
> To: Neena Susan Eappen <nee...@gm...>, pymol-users
> 	<pym...@li...>
> Subject: Re: [PyMOL] View two proteins from one pdb file
> Message-ID:
> 	<0c9...@it...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Neena,
> 
> Use the command ?split_states clusters?, just type it into the command line
> 
> J
> 
> From: Neena Susan Eappen <nee...@gm...>
> Sent: Monday, 8 June 2020 10:01 am
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] View two proteins from one pdb file
> 
> Hello PyMOL users,
> 
> I have a PDB file with coordinates for two proteins listed one after another (attached). However, when i open the file on pymol, I only see one protein (shown below) or it might be a sum of those 2 coordinates. How to view both structures?
> 
> [image.png]
> 
> Many thanks, and Take care,
> Neena
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> 
> ------------------------------
> 
> 
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> PyMOL-users mailing list
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> End of PyMOL-users Digest, Vol 169, Issue 9
> *******************************************

Re: [PyMOL] ramachandran plots

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

Never used but this plugin does Ramachandran plot.
https://pymolwiki.org/index.php/Dynoplot

Em ter., 9 de jun. de 2020 às 17:26, Thomas Charles Pochapsky <
poc...@br...> escreveu:

> Is there a plug-in or command that will output a Ramachandran plot for a
> loaded PDB file?
>
> Thanks,
>
> Tom Pochapsky
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 
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] ramachandran plots

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

Is there a plug-in or command that will output a Ramachandran plot for a 
loaded PDB file?

Thanks,

Tom Pochapsky

[PyMOL] User data

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

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

Re: [PyMOL] View two proteins from one pdb file

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

Thank you Saurabh, that also worked!

On Sun, 7 Jun 2020 at 18:23, Saurabh Gayali <sau...@gm...>
wrote:

> Hello Neena,
>
> Kindly note that the molecules have added up as frames. as evident from
> pymol [See screenshot below]. Use the next frame button to see next
> molecule.
> [image: image.png]
>
> I removed two lines from your pdb and both molecules are now coming in a
> single frame.
> [image: image.png]
>
> [image: image.png]
>
> I am attaching the resultant pdb file.
> I hope this could help you.
>
> ------------------------------
>
> *Saurabh Gayali* / Post Doctoral Fellow
> sau...@gm... / +91 8800412916
>
> *CSIR-IGIB*
> <http://example.com/>New Delhi, India
>
>
> On Mon, Jun 8, 2020 at 3:33 AM Neena Susan Eappen <nee...@gm...>
> wrote:
>
>> Hello PyMOL users,
>>
>> I have a PDB file with coordinates for two proteins listed one after
>> another (attached). However, when i open the file on pymol, I only see one
>> protein (shown below) or it might be a sum of those 2 coordinates. How to
>> view both structures?
>>
>> [image: image.png]
>>
>> Many thanks, and Take care,
>> 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] View two proteins from one pdb file

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

Thank Joel, that worked very well!

On Sun, 7 Jun 2020 at 18:28, Joel Tyndall <joe...@ot...> wrote:

> Hi Neena,
>
>
>
> Use the command “split_states clusters”, just type it into the command line
>
>
>
> J
>
>
>
> *From:* Neena Susan Eappen <nee...@gm...>
> *Sent:* Monday, 8 June 2020 10:01 am
> *To:* pymol-users <pym...@li...>
> *Subject:* [PyMOL] View two proteins from one pdb file
>
>
>
> Hello PyMOL users,
>
>
>
> I have a PDB file with coordinates for two proteins listed one after
> another (attached). However, when i open the file on pymol, I only see one
> protein (shown below) or it might be a sum of those 2 coordinates. How to
> view both structures?
>
>
>
> [image: image.png]
>
>
>
> Many thanks, and Take care,
>
> Neena
>

Re: [PyMOL] View two proteins from one pdb file

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

Hi Neena,

Use the command “split_states clusters”, just type it into the command line

J

From: Neena Susan Eappen <nee...@gm...>
Sent: Monday, 8 June 2020 10:01 am
To: pymol-users <pym...@li...>
Subject: [PyMOL] View two proteins from one pdb file

Hello PyMOL users,

I have a PDB file with coordinates for two proteins listed one after another (attached). However, when i open the file on pymol, I only see one protein (shown below) or it might be a sum of those 2 coordinates. How to view both structures?

[image.png]

Many thanks, and Take care,
Neena

Re: [PyMOL] View two proteins from one pdb file

[Saurabh G. <sau...@gm...>]

Hello Neena,

Kindly note that the molecules have added up as frames. as evident from
pymol [See screenshot below]. Use the next frame button to see next
molecule.
[image: image.png]

I removed two lines from your pdb and both molecules are now coming in a
single frame.
[image: image.png]

[image: image.png]

I am attaching the resultant pdb file.
I hope this could help you.

------------------------------

*Saurabh Gayali* / Post Doctoral Fellow
sau...@gm... / +91 8800412916

*CSIR-IGIB*
<http://example.com/>New Delhi, India


On Mon, Jun 8, 2020 at 3:33 AM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> I have a PDB file with coordinates for two proteins listed one after
> another (attached). However, when i open the file on pymol, I only see one
> protein (shown below) or it might be a sum of those 2 coordinates. How to
> view both structures?
>
> [image: image.png]
>
> Many thanks, and Take care,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] View two proteins from one pdb file

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

Hello PyMOL users,

I have a PDB file with coordinates for two proteins listed one after
another (attached). However, when i open the file on pymol, I only see one
protein (shown below) or it might be a sum of those 2 coordinates. How to
view both structures?

[image: image.png]

Many thanks, and Take care,
Neena

[PyMOL] Python 2 support removed from master branch

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

To those who compile Open-Source PyMOL from the github repo:

We've removed Python 2 support from the master branch, the master branch now requires Python 3.6 or later.

There is a new "py2" branch which marks the last Python 2 compatible state. We have no plans to actively maintain this legacy branch, but we will accept pull requests with bug fixes.

Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment

[Yong T. <liu...@gm...>]

Thanks Blaine and Thomas for the timely helps - what a life saver! Much
appreciated, -yong

On Thu, Jun 4, 2020 at 3:09 AM Thomas Holder <tho...@sc...>
wrote:

> Hi Yong and Blaine,
>
> The "alignto" command actually does allow you to specify the "mobile"
> objects.
>
> PyMOL>alignto ?
> Usage: alignto [ target [, method [, selection [, quiet ]]]]
>
> For example, you could disable all excluded objects and then use "enabled"
> as the selection:
>
> disable obj1 obj2 obj3
> alignto ref, super, enabled
>
> The alternative for such a heavy task would be a custom loop in Python:
>
> python
> for name in cmd.get_object_list():
>     if name != "ref":
>         cmd.super(name, "ref")
> python end
>
>
> By the way, "alignto" is just a wrapper for "extra_fit", with different
> argument order and default arguments. See also:
> https://pymolwiki.org/index.php/Extra_fit
>
> Cheers,
>   Thomas
>
> > On Jun 4, 2020, at 12:12 AM, Mooers, Blaine H.M. (HSC) <
> Bla...@ou...> wrote:
> >
> > Hi Yong,
> >
> > Maybe you tried this already, but you might try reducing the use of RAM
> by superposing all 500 structures represented as CA traces
> > ('ribbons' in PyMOL) or even show the  CA atoms as lines (show lines,
> name ca and i. *) and then switch representation after alignment.
> >
> > Best regards,
> >
> > Blaine
> >
> > Blaine Mooers, Ph.D.
> > Associate Professor
> > University of Oklahoma Health Sciences Center
> > Oklahoma City, OK 73104-5419
> >
> > ________________________________________
> > From: Yong Tang [liu...@gm...]
> > Sent: Wednesday, June 03, 2020 3:55 PM
> > To: pym...@li...
> > Subject: [EXTERNAL] [PyMOL] protecting a group during subsequent aligment
> >
> > Dear all, I have a task to overlay 500+ structures onto a reference
> structure "ref", as the body of data is big, I decided to do them in
> chunks, 100 at a time (after crashing pymol on my Windows laptop for a few
> times attempting it). This is the commend that I used for the first 100:
> >
> > alignto ref, method=super.
> >
> > This worked perfectly for most entries, but not for all, so I manually
> adjusted some entries, and then grouped them into chunck1.
> >
> > Now I'm ready to move on to the next chunk; I realized I wanted to
> protect the processed entries from being moved/aligned again as the alignto
> doesn't allow specification of the "mobile". I applied the
> /Actions/Movement/Protect on group chunk1, but that didn't seem to prevent
> the entries in there to be moved/aligned again.
> >
> > Any clue how to fix my problem?
> >
> > Many thanks, -yong
> >
> >
> > _______________________________________________
> > 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.
>
>

Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment

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

Hi Yong and Blaine,

The "alignto" command actually does allow you to specify the "mobile" objects.

PyMOL>alignto ?
Usage: alignto [ target [, method [, selection [, quiet ]]]]

For example, you could disable all excluded objects and then use "enabled" as the selection:

disable obj1 obj2 obj3
alignto ref, super, enabled

The alternative for such a heavy task would be a custom loop in Python:

python
for name in cmd.get_object_list():
    if name != "ref":
        cmd.super(name, "ref")
python end


By the way, "alignto" is just a wrapper for "extra_fit", with different argument order and default arguments. See also:
https://pymolwiki.org/index.php/Extra_fit

Cheers,
  Thomas

> On Jun 4, 2020, at 12:12 AM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> 
> Hi Yong, 
> 
> Maybe you tried this already, but you might try reducing the use of RAM by superposing all 500 structures represented as CA traces 
> ('ribbons' in PyMOL) or even show the  CA atoms as lines (show lines, name ca and i. *) and then switch representation after alignment. 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> University of Oklahoma Health Sciences Center
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Yong Tang [liu...@gm...]
> Sent: Wednesday, June 03, 2020 3:55 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] protecting a group during subsequent aligment
> 
> Dear all, I have a task to overlay 500+ structures onto a reference structure "ref", as the body of data is big, I decided to do them in chunks, 100 at a time (after crashing pymol on my Windows laptop for a few times attempting it). This is the commend that I used for the first 100:
> 
> alignto ref, method=super.
> 
> This worked perfectly for most entries, but not for all, so I manually adjusted some entries, and then grouped them into chunck1.
> 
> Now I'm ready to move on to the next chunk; I realized I wanted to protect the processed entries from being moved/aligned again as the alignto doesn't allow specification of the "mobile". I applied the /Actions/Movement/Protect on group chunk1, but that didn't seem to prevent the entries in there to be moved/aligned again.
> 
> Any clue how to fix my problem?
> 
> Many thanks, -yong
> 
> 
> _______________________________________________
> 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.

Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment

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

Hi Yong, 

Maybe you tried this already, but you might try reducing the use of RAM by superposing all 500 structures represented as CA traces 
('ribbons' in PyMOL) or even show the  CA atoms as lines (show lines, name ca and i. *) and then switch representation after alignment. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
University of Oklahoma Health Sciences Center
Oklahoma City, OK 73104-5419

________________________________________
From: Yong Tang [liu...@gm...]
Sent: Wednesday, June 03, 2020 3:55 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] protecting a group during subsequent aligment

Dear all, I have a task to overlay 500+ structures onto a reference structure "ref", as the body of data is big, I decided to do them in chunks, 100 at a time (after crashing pymol on my Windows laptop for a few times attempting it). This is the commend that I used for the first 100:

alignto ref, method=super.

This worked perfectly for most entries, but not for all, so I manually adjusted some entries, and then grouped them into chunck1.

Now I'm ready to move on to the next chunk; I realized I wanted to protect the processed entries from being moved/aligned again as the alignto doesn't allow specification of the "mobile". I applied the /Actions/Movement/Protect on group chunk1, but that didn't seem to prevent the entries in there to be moved/aligned again.

Any clue how to fix my problem?

Many thanks, -yong

Re: [PyMOL] [EXTERNAL] Changing Chain ID

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

Hi Patricia,

You can add unique segment identifiers to each actin.
https://www.biostars.org/p/129381/

You can add these segids by using column selection in 
a text editor like Visual Studio Code, which is free. 
Install the BioSyntax plugin to get syntax highlighting 
of the pdb file. 


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: pat...@lo... [pat...@lo...]
Sent: Wednesday, June 03, 2020 12:45 PM
To: pym...@li...
Subject: Re: [PyMOL] [EXTERNAL]  Changing Chain ID

Thank you Dr. Mooers,

That worked! I’ve been trying to solve that for months. I’ve been able to get my protein, linker and actin to fuse.

I have now built a chain of five actin and I’m encountering another barrier. I’m attempting to link a protein to each actin, but the program recognizes all 5 linkers as the same linker (all linkers have the same sequence). I’m trying to figure out how to give each linker its own separate name. I’ve searched the mailing group archive and looked at the Alter page you linked for the first solution, but can’t figure out what to do.

If you have any further advice that would be much appreciated!

Patricia



On Tue, 2 Jun 2020 17:49:05 +0000, "Mooers, Blaine H.M. (HSC)" <Bla...@ou...> wrote:

Hi Patricia,

You can copy and paste these commands below one at a time at the upper PyMOL> prompt just below the command history window.
Hit return after each paste operation.

alter (chain A),chain='F'
sort

For more information, see https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php-3Ftitle-3DAlter-26redirect-3Dno&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=J3kxkoyQ22CsHFbJcbFrSLohew1yxUPoqMUzfIEHcJU&s=aCIVpCaJYi7T-Ulchmsmp-zOn4dqPHLlwh4sCs8RAAA&e=

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: pat...@lo... [pat...@lo...]
Sent: Tuesday, June 02, 2020 11:49 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Changing Chain ID

Hi – I’m a high school student learning to use Pymol for my science fair research, and I’ve been using Pymol for about 6 months. I have been working on attempting to bind a protein to actin for over a month now – but whenever I fuse the linker to the antifreeze protein, it glitches. As well, when I save my actin chain with all the linkers fused as a PDB file and reopen it, only one of the linkers is visible. I’m hoping you might be able to help me figure out what I’m doing wrong.

Schrodenger support provided a recommendation. Part of it is to rename the protein chain to something else (e.g., chain F) so that it wouldn't interfere with chain A from the F-Actin chain. I’ve been unable to figure out how to change the name/ID of my chains. I have tried changing to “3 Button Viewing”, selecting “Chains”, clicking on the chain of interest, clicking on the selection “A” action button and selecting “rename selection”, as well as using the "set_name" command, but neither are working.

Can anyone help me figure out what I’m doing wrong?

Thanks so much!


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[PyMOL] protecting a group during subsequent aligment

[Yong T. <liu...@gm...>]

Dear all, I have a task to overlay 500+ structures onto a reference
structure "ref", as the body of data is big, I decided to do them in
chunks, 100 at a time (after crashing pymol on my Windows laptop for a few
times attempting it). This is the commend that I used for the first 100:

alignto ref, method=super.

This worked perfectly for most entries, but not for all, so I manually
adjusted some entries, and then grouped them into chunck1.

Now I'm ready to move on to the next chunk; I realized I wanted to protect
the processed entries from being moved/aligned again as the alignto doesn't
allow specification of the "mobile". I applied the
/Actions/Movement/Protect on group chunk1, but that didn't seem to prevent
the entries in there to be moved/aligned again.

Any clue how to fix my problem?

Many thanks, -yong

Re: [PyMOL] [EXTERNAL] Changing Chain ID

[<pat...@lo...>]

Thank you Dr. Mooers,

That worked! I’ve been trying to solve that for months. I’ve been able to get my protein, linker and actin to fuse.

I have now built a chain of five actin and I’m encountering another barrier. I’m attempting to link a protein to each actin, but the program recognizes all 5 linkers as the same linker (all linkers have the same sequence). I’m trying to figure out how to give each linker its own separate name. I’ve searched the mailing group archive and looked at the Alter page you linked for the first solution, but can’t figure out what to do.

If you have any further advice that would be much appreciated!

Patricia



On Tue, 2 Jun 2020 17:49:05 +0000, "Mooers, Blaine H.M. (HSC)" <Bla...@ou...> wrote:

Hi Patricia,

You can copy and paste these commands below one at a time at the upper PyMOL> prompt just below the command history window.
Hit return after each paste operation.

alter (chain A),chain='F'
sort

For more information, see https://pymolwiki.org/index.php?title=Alter&redirect=no

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: pat...@lo... [pat...@lo...]
Sent: Tuesday, June 02, 2020 11:49 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Changing Chain ID

Hi – I’m a high school student learning to use Pymol for my science fair research, and I’ve been using Pymol for about 6 months. I have been working on attempting to bind a protein to actin for over a month now – but whenever I fuse the linker to the antifreeze protein, it glitches. As well, when I save my actin chain with all the linkers fused as a PDB file and reopen it, only one of the linkers is visible. I’m hoping you might be able to help me figure out what I’m doing wrong.

Schrodenger support provided a recommendation. Part of it is to rename the protein chain to something else (e.g., chain F) so that it wouldn't interfere with chain A from the F-Actin chain. I’ve been unable to figure out how to change the name/ID of my chains. I have tried changing to “3 Button Viewing”, selecting “Chains”, clicking on the chain of interest, clicking on the selection “A” action button and selecting “rename selection”, as well as using the "set_name" command, but neither are working.

Can anyone help me figure out what I’m doing wrong?

Thanks so much!


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Re: [PyMOL] [EXTERNAL] Changing Chain ID

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

Hi  Patricia,

You can copy and paste these commands below one at a time at the upper PyMOL> prompt just below the command history window.
Hit return after each paste operation.

alter (chain A),chain='F'
sort

For more information, see https://pymolwiki.org/index.php?title=Alter&redirect=no

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: pat...@lo... [pat...@lo...]
Sent: Tuesday, June 02, 2020 11:49 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Changing Chain ID

Hi – I’m a high school student learning to use Pymol for my science fair research, and I’ve been using Pymol for about 6 months. I have been working on attempting to bind a protein to actin for over a month now – but whenever I fuse the linker to the antifreeze protein, it glitches. As well, when I save my actin chain with all the linkers fused as a PDB file and reopen it, only one of the linkers is visible. I’m hoping you might be able to help me figure out what I’m doing wrong.

Schrodenger support provided a recommendation. Part of it is to rename the protein chain to something else (e.g., chain F) so that it wouldn't interfere with chain A from the F-Actin chain. I’ve been unable to figure out how to change the name/ID of my chains. I have tried changing to “3 Button Viewing”, selecting “Chains”, clicking on the chain of interest, clicking on the selection “A” action button and selecting “rename selection”, as well as using the "set_name" command, but neither are working.

Can anyone help me figure out what I’m doing wrong?

Thanks so much!


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[PyMOL] Changing Chain ID

[<pat...@lo...>]

Hi – I’m a high school student learning to use Pymol for my science fair research, and I’ve been using Pymol for about 6 months. I have been working on attempting to bind a protein to actin for over a month now – but whenever I fuse the linker to the antifreeze protein, it glitches. As well, when I save my actin chain with all the linkers fused as a PDB file and reopen it, only one of the linkers is visible. I’m hoping you might be able to help me figure out what I’m doing wrong.

Schrodenger support provided a recommendation. Part of it is to rename the protein chain to something else (e.g., chain F) so that it wouldn't interfere with chain A from the F-Actin chain. I’ve been unable to figure out how to change the name/ID of my chains. I have tried changing to “3 Button Viewing”, selecting “Chains”, clicking on the chain of interest, clicking on the selection “A” action button and selecting “rename selection”, as well as using the "set_name" command, but neither are working.

Can anyone help me figure out what I’m doing wrong?

Thanks so much!

Re: [PyMOL] [EXTERNAL] Numpy for Pymod

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

Hi Juliet,

It would help others to report more specifics like the version of PyMOL that you are using
(it is printed on the first line in the command history window 
when you start PyMOL) and whether it is the incentive product or open source.

I suspect that the Python interpreter that runs your PyMOL
is not the same as the Python interpreter for which you installed numpy.
The PyMOL Python is not finding your recently installed numpy installation. 

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: Juliet Lee [ja...@ba...]
Sent: Monday, June 01, 2020 5:07 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Numpy for Pymod

Hello,
I am trying to use Pymod on Pymol and have successfully installed Pymod as a plugin in pymol.
But when I try to open Pymod 3, it tells me that "NumPy is not installed on your system."
I tried to install Numpy in Mac Terminal and I think I did but it is still not working.
Thank you for any help with this most likely very basic question.

[PyMOL] Numpy for Pymod

[Juliet L. <ja...@ba...>]

Hello,
I am trying to use Pymod on Pymol and have successfully installed Pymod as
a plugin in pymol.
But when I try to open Pymod 3, it tells me that "NumPy is not installed on
your system."
I tried to install Numpy in Mac Terminal and I think I did but it is still
not working.
Thank you for any help with this most likely very basic question.

[PyMOL] Molecular Docking

[Grace C. <go...@le...>]

Hello,
Has anyone used NRGSuites as a PyMol Plugin? I'm using xquartz to
facilitate it, however when I try to switch from the input tab to the
configure target/configure ligand tabs within the FlexAid section of the
plugin I get an error "Cannot switch tab: could not kill the frame" and I
do not know how to fix it. I think it could be a python error?
If not, can someone suggest a user friendly docking software which I can
use as a PyMol plugin to conduct docking/binding assays on a Mac?
Thank you,
Grace

[PyMOL] Automatic Video generation

[Mohamed A. <m.b...@gm...>]

Hello everybody,

I am doing molecular simulation using GROMACS program and I visualize the
output (.pdb) using Pymol. I am inserting 4000 molecule inside a box, one
molecule at a time,  and after every insertion I convert the output into a
.pdb file so at the end I have 4000 .pdb file. I want to generate a video
to see where each new atom is inserted. This means that I need to open
(load) the 4000 file and then display them in a sequence so that each new
molecule will be clear where it was inserted. can you please guide me how
to do that ?

I am using Ubuntu system and I always open pymol using the interface (not
the terminal). I have searched online how can I do that, but I didn't find
how to do it.

Can you please help me.

Many thanks,
Mohamed