pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)

[ahoneg <ann...@uz...>]

Dear Bruce

Try the SwissSidechain PyMOL plugin and database

https://www.swisssidechain.ch/visualization/pymol.php

Annemarie
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     



> On 22 Jul 2019, at 14:02, pym...@li... wrote:
> 
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
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> or, via email, send a message with subject or body 'help' to
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> Today's Topics:
> 
>   1. amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 21 Jul 2019 22:02:08 -0700
> From: Bruce Onisko <bco...@gm...>
> To: pym...@li...
> Subject: [PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs?
> Message-ID:
> 	<CANFKuAo=JQw...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> I need to 'mutate" a residue of a protein to a hydroxyproline, aka HYP.
> 
> In Wizard|Mutagenesis, I see how to choose 1 of about 20 other amino acids,
> but I hydroxyproline is not in the list.
> 
> Does anyone know how I create such an entry?
> 
> Or should I learn how to edit a proline?  (Using Builder I assume?)
> 
> Anyone creating post-translational modifications (eg SER-O-phosphate) would
> have a similar question........
> 
> Thanks!
> 
> Bruce
> 
> PS \PyMOL\share\pymol\data\chempy\fragments\ has all the amino acids, but
> not what i need.
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> End of PyMOL-users Digest, Vol 158, Issue 17
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[PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs?

[Bruce O. <bco...@gm...>]

Hi all,

I need to 'mutate" a residue of a protein to a hydroxyproline, aka HYP.

In Wizard|Mutagenesis, I see how to choose 1 of about 20 other amino acids,
but I hydroxyproline is not in the list.

Does anyone know how I create such an entry?

Or should I learn how to edit a proline?  (Using Builder I assume?)

Anyone creating post-translational modifications (eg SER-O-phosphate) would
have a similar question........

Thanks!

Bruce

PS \PyMOL\share\pymol\data\chempy\fragments\ has all the amino acids, but
not what i need.

Re: [PyMOL] [EXTERNAL] Re: Skip Activation Window Remove

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

There are three pymol Wiki pages that describe how to install open-source PyMOL on Linus, Windows, and Mac.

https://pymolwiki.org/index.php/Linux_Install
https://pymolwiki.org/index.php/Windows_Install
https://pymolwiki.org/index.php/MAC_Install

I have installed open-source PyMOL on Windows10, Ubuntu, and Mac with macports ( sudo port install pymol).
Home-brew and fink are addition repositories of the binaries for the Mac.
Macports does a good job of keeping the pymol port current. 

The open-source PyMOL in Ubuntu's main software repository has been out-of-date in the past. 
I recommend instead using Troels Linnet's installations script  https://pymolwiki.org/index.php/User:Tlinnet/Linux_Install.

The installation of macports requires Xcode and the Xcode command line tools. 
Here is a current guide for installing PyMOL with homebrew: https://quantixed.org/2019/02/16/installing-open-source-pymol-on-a-mac/. 
I have never had success building PyMOL from source on the Mac. 

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: Rohan Eapen [rs...@ca...]
Sent: Thursday, July 18, 2019 4:08 AM
To: Neena Susan Eappen
Cc: pym...@li...
Subject: [EXTERNAL] Re: [PyMOL] Skip Activation Window Remove

I tend to use the open source versions. They're free, i.e no license file is needed.

If you're on windows, here's a simple guide on how to install a pre-compiled version of it. https://www.biob.in/2016/09/installing-latest-pymol-software-for.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biob.in_2016_09_installing-2Dlatest-2Dpymol-2Dsoftware-2Dfor.html&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=8_b1lrMJpUIemHtpLPBQRCs19KN9Sf-oAcJWb0R7LUc&s=LjQJQLjK5pyzJpR8eXi90YOYhr8qK1PiLFFN3q6_pTU&e=>

Best wishes,
Rohan

On Thu, 18 Jul 2019 at 01:15, Neena Susan Eappen <nee...@gm...<mailto:nee...@gm...>> wrote:
Hello PyMOL users,

I have been using official PyMOL build which requires a license. I do not need any special features of pymol, is there a way to remove this 'No License File' window?

Many thanks,
Neena
_______________________________________________
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--
Rohan Eapen
Itzhaki group - PhD student
Department of Pharmacology
University of Cambridge
Tennis Court Road
CB2 1PD
rs...@ca...<mailto:rs...@ca...>

Re: [PyMOL] Skip Activation Window Remove

[Rohan E. <rs...@ca...>]

I tend to use the open source versions. They're free, i.e no license file
is needed.

If you're on windows, here's a simple guide on how to install a
pre-compiled version of it.
https://www.biob.in/2016/09/installing-latest-pymol-software-for.html

Best wishes,
Rohan

On Thu, 18 Jul 2019 at 01:15, Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> I have been using official PyMOL build which requires a license. I do not
> need any special features of pymol, is there a way to remove this 'No
> License File' window?
>
> 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



-- 
Rohan Eapen
Itzhaki group - PhD student
Department of Pharmacology
University of Cambridge
Tennis Court Road
CB2 1PD
rs...@ca...

Re: [PyMOL] Skip Activation Window Remove

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

You can always use the Educational version of Pymol.
Regards,
*Saurabh Gayali*
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On Thu, Jul 18, 2019 at 5:46 AM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> I have been using official PyMOL build which requires a license. I do not
> need any special features of pymol, is there a way to remove this 'No
> License File' window?
>
> 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

[PyMOL] Skip Activation Window Remove

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

Hello PyMOL users,

I have been using official PyMOL build which requires a license. I do not
need any special features of pymol, is there a way to remove this 'No
License File' window?

Many thanks,
Neena

Re: [PyMOL] Plugin upload.

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

Hi Will,

You need a GPL-compatible license for your plugin which uses PyQt. This could be GPL (of course) but also BSD-3-Clause or Apache License.

By the way, PyMOL also works with PySide (which is LGPL). So strictly speaking, your plugin will not depend on PyQt, you could always set up Open-Source PyMOL with PySide and use that instead. The compatibility module is pymol.Qt (do "from pymol.Qt import QtWidgets" instead of "from PyQt5 import QtWidgets").

Hope that helps.

Cheers,
  Thomas

> On Jul 11, 2019, at 3:53 PM, William Tao <ywt...@gm...> wrote:
> 
> Hi Wael,
> 
> I'm somehow curious whether you have used PyQt in your plugin. 
> 
> Nowadays, people usually upload released code onto repositories like GitHub. But I'm not sure which open source license we need to use if PyQt is used. 
> 
> Hope anyone who is familiar with this issue could help.
> 
> Many thanks.
> 
> Will
> 
> 
> Wael Azzam via PyMOL-users <pym...@li...> 于2019年7月9日周二 上午3:11写道：
> To whom it may concern,
> 
> I am writing to you in the hopes of knowing how to upload a PyMol plugin that I developed on the page PyMolWiki ?
> 
> Best regards,
> 
> Wael Azzam
> B.S in Bioinformatics 
> Lebanese American University, Beirut

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Plugin upload.

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

Hi Wael,

Of course you can add it to the PyMOLWiki!

If your plugin is a single Python file, then the easiest thing to do is to add it to the Pymol-script-repo. Just fork https://github.com/Pymol-Scripts/Pymol-script-repo and make a pull request.

If your plugin is more complex (multiple files), then it will be better if you make your own github project for it. Users can download your repo as a ZIP file from github and install that zip file with PyMOL's plugin manager (if you follow a layout like https://github.com/Pymol-Scripts/pymol2-demo-plugin ).

In addition to uploading your plugin to github, you should create a page on the PyMOLWiki with instructions how to use it.

Cheers,
  Thomas


> On Jul 11, 2019, at 10:10 PM, Wael Azzam via PyMOL-users <pym...@li...> wrote:
> 
> Hello Will,
> 
> Thank you for your reply!!
> 
> No, I used Tkinter for Gui with no implementation of PyQt whatsoever.
> So, i cannot make it to the PyMolWiki plugins category?
> 
> Best,
> Wael
> 
> 
> 
> On 11 Jul,2019, at 16:53, William Tao <ywt...@gm...> wrote:
> 
>> Hi Wael,
>> 
>> I'm somehow curious whether you have used PyQt in your plugin. 
>> 
>> Nowadays, people usually upload released code onto repositories like GitHub. But I'm not sure which open source license we need to use if PyQt is used. 
>> 
>> Hope anyone who is familiar with this issue could help.
>> 
>> Many thanks.
>> 
>> Will
>> 
>> 
>> Wael Azzam via PyMOL-users <pym...@li...> 于2019年7月9日周二 上午3:11写道：
>> To whom it may concern,
>> 
>> I am writing to you in the hopes of knowing how to upload a PyMol plugin that I developed on the page PyMolWiki ?
>> 
>> Best regards,
>> 
>> Wael Azzam
>> B.S in Bioinformatics 
>> Lebanese American University, Beirut

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Plugin upload.

[Wael A. <wae...@ic...>]

Hello Will,

Thank you for your reply!!

No, I used Tkinter for Gui with no implementation of PyQt whatsoever.
So, i cannot make it to the PyMolWiki plugins category?

Best,
Wael



> On 11 Jul,2019, at 16:53, William Tao <ywt...@gm...> wrote:
> 
> Hi Wael,
> 
> I'm somehow curious whether you have used PyQt in your plugin. 
> 
> Nowadays, people usually upload released code onto repositories like GitHub. But I'm not sure which open source license we need to use if PyQt is used. 
> 
> Hope anyone who is familiar with this issue could help.
> 
> Many thanks.
> 
> Will
> 
> 
> Wael Azzam via PyMOL-users <pym...@li...> 于2019年7月9日周二 上午3:11写道：
>> To whom it may concern,
>> 
>> I am writing to you in the hopes of knowing how to upload a PyMol plugin that I developed on the page PyMolWiki ?
>> 
>> Best regards,
>> 
>> Wael Azzam
>> B.S in Bioinformatics 
>> Lebanese American University, Beirut
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Plugin upload.

[William T. <ywt...@gm...>]

Hi Wael,

I'm somehow curious whether you have used PyQt in your plugin.

Nowadays, people usually upload released code onto repositories like
GitHub. But I'm not sure which open source license we need to use if PyQt
is used.

Hope anyone who is familiar with this issue could help.

Many thanks.

Will


Wael Azzam via PyMOL-users <pym...@li...> 于2019年7月9日周二
上午3:11写道：

> To whom it may concern,
>
> I am writing to you in the hopes of knowing how to upload a PyMol plugin
> that I developed on the page PyMolWiki ?
>
> Best regards,
>
> Wael Azzam
> B.S in Bioinformatics
> Lebanese American University, Beirut
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] PyMOL-users Digest, Vol 158, Issue 13

[ahoneg <ann...@uz...>]

Dear sunyeping

The critical step in calculating a 3D superposition is the decision of which atom in one structure to fit on which atom in the second structure.
Actually fitting the transformation matrix is trivial in comparison. 

In PyMOL you have different ways to determine what you fit:
If you use “pairfit” or “super”, you explicitly tell the program which atoms to fit to which, and you will get an error message if the two selections do not contain exactly the same number of atoms, e.g. because if you have alternative locations for some of the atoms.

Super will generate an initial 3D alignment and then iteratively improve the alignment by eliminating the atom pairs that show the highest divergence. This generates a 3D alignment that concentrates on the structural core and ignores highly flexible loops: This is ideal to generate an image that illustrates that two proteins are structurally related, but will not give you a highly reproducible rmsd value that you can compare, because you do not exactly know what has been fitted. 
With pairfit, you know exactly which atoms are fitted to which, but it can be tedious to enumerate  exactly all the atoms you want to fit. Its advantag is that in comparing a whole series of structures, you can force it to compare exactly the same part of the structures and thereby get rmsd values you can compare even if the labels are not identical in the two structures, because you explicitly tell the program which atoms to pair for the fit.
Fit relies on corresponding atoms having the same label in the two structures. 
Align uses a sequence alignment to identify corresponding atoms (look carefully at the sequence alignment and the alignment object to check whether this makes sense), it works well for comparing snapshots of the same protein along a dynamics run or for proteins with identical or at least very similar sequence, while cealign iteratively optimizes the atom pairing to achieve a sequence-independent structural alignment, and thereby is able to give you a fairly robust alignment of two structures with divergent sequences but similar structures, e.g. GPCRs or antibodies.

Which method you use depends on the purpose of your alignment (illustration of similarity versus quantification of the goodness of the fit),
the sequence similarity and the structural similarity of the two or more structures you are comparing. You also have to decide if you do an all-atom fit, if you want to fit only the backbone atoms, or only the “guide atoms” (Calpha in the case of proteins, C4’ for nucleic acid). In any case, if are citing rmsd values, you have to indicate clearly what you have been doing, otherwise a comparison of rmsd values is meaningless.

best regards

Annemarie

____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     



> On 11 Jul 2019, at 14:01, 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. about cealign and align (sunyeping)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 11 Jul 2019 10:12:31 +0800
> From: "sunyeping" <sun...@al...>
> To: "pymol-users" <pym...@li...>
> Subject: [PyMOL] about cealign and align
> Message-ID:
> 	<4c1...@al...>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear all,
> 
> I am now trying to compare two structures by alignment in pymol. The two proteins are similar structures from the same family with about 500 residues. I find that the "cealign" command gives much better result that the "align" command. With the "cealign" command, the two structures aligned well, but with "align" command two structure don't aligned well. The rmsd value given with the "cealign" is much smaller than that given with the "align". 
> 
> However, when I try the align a small region of the two structures, I get the reverse result. I create new objects corresponding to the small region I am interested in from the two whole proteins, respectively and align the two new objects with "align" and "cealign". I find the rmsd value given with "align" is much smaller that than given with "cealign". 
> 
> I wish know the work principle behind "align" and "celign", the calculation formula of them and what cause the difference between aligning the whole proteins and small regions. Could you help me with these?
> 
> Best regards.
> -------------- next part --------------
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> End of PyMOL-users Digest, Vol 158, Issue 13
> ********************************************

[PyMOL] about cealign and align

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

Dear all,

I am now trying to compare two structures by alignment in pymol. The two proteins are similar structures from the same family with about 500 residues. I find that the "cealign" command gives much better result that the "align" command. With the "cealign" command, the two structures aligned well, but with "align" command two structure don't aligned well. The rmsd value given with the "cealign" is much smaller than that given with the "align". 

However, when I try the align a small region of the two structures, I get the reverse result. I create new objects corresponding to the small region I am interested in from the two whole proteins, respectively and align the two new objects with "align" and "cealign". I find the rmsd value given with "align" is much smaller that than given with "cealign". 

I wish know the work principle behind "align" and "celign", the calculation formula of them and what cause the difference between aligning the whole proteins and small regions. Could you help me with these?

Best regards.

Re: [PyMOL] Align more than two structures

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

extra_fit aligns multiple objects to a reference object.


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



Regards,
*Saurabh Gayali*
---------------------------------------------------------------------


On Wed, Jul 10, 2019 at 9:25 AM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> How to align more than two structures in pymol?
>
> Thank you,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Align more than two structures

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

Hello PyMOL users,

How to align more than two structures in pymol?

Thank you,
Neena

Re: [PyMOL] Search error in PyMOLWiki

[Jason K. <ke...@hk...>]

Hi Timofey,

This should be fixed now.
Please let me know if you find otherwise.

Cheers,
Jason

-- 
*Jason Key, PhD*
Structural Biology Grid   - SBGrid.org <http://sbgrid.org/>
Harvard Medical School - hms.harvard.edu

Re: [PyMOL] The 'select' command for complex residue selection

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

The last parentheses is not the ASCII character ")" (code 41), but the unicode character "）" (code U+FF09) and PyMOL can't handle that.

https://www.compart.com/en/unicode/U+FF09

Cheers,
  Thomas


> On Jul 9, 2019, at 5:47 AM, Kevin Jude <kj...@st...> wrote:
> 
> Strange, I get the same error and can't figure out why it doesn't like the parentheses around the second term, though here are a few formulations that give the correct result without syntax errors:
> 
>  select sele, protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119) or protein_A and chain C and resi 87-95
>  select sele, (protein_A and chain C and resi 87-95) or (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119))
>  select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119))
>  select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A and resi 29-33 or resi 70-73 or resi 116-119)
> 
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
> 
> On Mon, Jul 8, 2019 at 7:40 PM sunyeping via PyMOL-users <pym...@li...> wrote:
> Dear all, 
> 
> In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following:
> 
>    select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95）
> 
> but it returns syntax error. So what is the correct command for this?
> 
> Thank you in advance

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] The 'select' command for complex residue selection

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

Hi, Ali,

Your command format works well. Thank you.
------------------------------------------------------------------
From:Ali Kusay <aku...@un...>
Sent At:2019 Jul. 9 (Tue.) 11:11
To:孙业平 <sun...@al...>
Cc:pymol-users <pym...@li...>
Subject:Re: [PyMOL] The 'select' command for complex residue selection


Hi Sunyeping,
I am not sure where your error is coming from (I noticed you also wrote protein_A in second selection as well). I have however rewritten the command in a simpler way, so try this:
select sele, (protein_A and c. A and resi 29-33+70-73+116-119) or (protein_B and c. C and resi 87-95)
c. A is equivalent to chain A and this residue selection formats avoid the need of annoying “or” statements
Cheers,
Ali
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: aku...@un...
From: sunyeping via PyMOL-users <pym...@li...>
Reply-To: sunyeping <sun...@al...>
Date: Tuesday, 9 July 2019 at 12:41 pm
To: pymol-users <pym...@li...>
Subject: [PyMOL] The 'select' command for complex residue selection
Dear all, 
In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following:
   select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95）
but it returns syntax error. So what is the correct command for this?
Thank you in advance

Re: [PyMOL] The 'select' command for complex residue selection

[Kevin J. <kj...@st...>]

Strange, I get the same error and can't figure out why it doesn't like the
parentheses around the second term, though here are a few formulations that
give the correct result without syntax errors:

 select sele, protein_A and chain A and (resi 29-33 or resi 70-73 or resi
116-119) or protein_A and chain C and resi 87-95
 select sele, (protein_A and chain C and resi 87-95) or (protein_A and
chain A and (resi 29-33 or resi 70-73 or resi 116-119))
 select sele, protein_A and chain C and resi 87-95 or (protein_A and chain
A and (resi 29-33 or resi 70-73 or resi 116-119))
 select sele, protein_A and chain C and resi 87-95 or (protein_A and chain
A and resi 29-33 or resi 70-73 or resi 116-119)

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Mon, Jul 8, 2019 at 7:40 PM sunyeping via PyMOL-users <
pym...@li...> wrote:

> Dear all,
>
> In pymol I loaded two protein: protein_A and protein_B. I want to make a
> selection of some incontinuous residues from two chains of protein_A, for
> example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96
> from chain C. How should I write the select command? I tried the following:
>
>    select sele, (protein_A
> and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A
> and chain C and resi 87-95）
>
> but it returns syntax error. So what is the correct command for this?
>
> Thank you in advance
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] The 'select' command for complex residue selection

[Ali K. <aku...@un...>]

Hi Sunyeping,

I am not sure where your error is coming from (I noticed you also wrote protein_A in second selection as well). I have however rewritten the command in a simpler way, so try this:

select sele, (protein_A and c. A and resi 29-33+70-73+116-119) or (protein_B and c. C and resi 87-95)

c. A is equivalent to chain A and this residue selection formats avoid the need of annoying “or” statements

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: aku...@un...

From: sunyeping via PyMOL-users <pym...@li...>
Reply-To: sunyeping <sun...@al...>
Date: Tuesday, 9 July 2019 at 12:41 pm
To: pymol-users <pym...@li...>
Subject: [PyMOL] The 'select' command for complex residue selection

Dear all,

In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following:

   select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95）

but it returns syntax error. So what is the correct command for this?

Thank you in advance

[PyMOL] The 'select' command for complex residue selection

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

Dear all, 

In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following:

   select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95）

but it returns syntax error. So what is the correct command for this?

Thank you in advance

[PyMOL] How to calculate RMSD among multiple proteins

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

Dear all,

It is easy to evaluate the simularity of two proteins in pymol. We just need to align them and a RMSD will be given in pymol. However, I want to compare the strutural similiarity of multiple proteins. I can align two of them once and by doing alignment many times, I can finally get pair-wise RMSD of these proteins. Is there any simple method to do? Is there a scriipt that can automatically calculate the pair-wise RMSD among many proteins in pymol?

Thank you in advance. 

Re: [PyMOL] How to label secondary structures in pymol

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

Thank you, Jared.
------------------------------------------------------------------
From:Jared Sampson <jar...@co...>
Sent At:2019 Jul. 8 (Mon.) 12:08
To:pymol-users <pym...@li...>; 孙业平 <sun...@al...>
Subject:Re: [PyMOL] How to label secondary structures in pymol


Hi sunyeping - 

Yes, it is possible.  You can pick one atom to label in each SS element.  See this old thread: https://sourceforge.net/p/pymol/mailman/message/30823352/. 

You can also adjust the label position/size/style using the various label settings as well.  I would normally direct you to the label wiki page, but that appears (at least to me) to be broken at the moment.  So here, instead, is a link to a few-years-old archive of that page.

Hope that helps.

Cheers,
Jared 

On July 7, 2019 at 1:38:15 PM, sunyeping via PyMOL-users (pym...@li...) wrote:
 Dear all,

Is it possible to label  secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1",  "α2", "β2", etc..

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

Re: [PyMOL] PyMOL-users Digest, Vol 158, Issue 6

[ahoneg <ann...@uz...>]

Dear Yeping 

You can color the surface independent of the atom color with the command

set surface_color, (color), (selection)

similarly, you color the cartoon representation dependent of the atom color with the command

set cartoon_color, (color), (selection)

best regards

Annemarie
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     


> 
> ---------------------------------------------------------------------
> 
> 
> 		I?m protected online with Avast Free Antivirus. Get it here ? it?s free forever.  
> On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users <pym...@li...> wrote:
> Dear all,
> 
> I color a protein as blue, display it by surface and cartoon simultaneously, and set the surface transperant so that the cartoon representation inside the surface can be seen. I display one residue as stick. I want to color the stick by element, but keep the surface representation as blue. However, I don't know how to do this. I can color the residue (please see the  Gln in the yellow circle at https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both the stick and the surface representations are colored by element. Could anyone tell me how to color stick representation of this Gln by element but keep its surface representation as blue?
> 
> Thank you in advance
> Yeping

[PyMOL] Plugin upload.

[Wael A. <wae...@ic...>]

To whom it may concern,

I am writing to you in the hopes of knowing how to upload a PyMol plugin that I developed on the page PyMolWiki ?

Best regards,

Wael Azzam
B.S in Bioinformatics 
Lebanese American University, Beirut

Re: [PyMOL] Errors in "Label" page on PyMOL Wiki

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

Hi Jared,

I can confirm this. There is a <math> tag in the page, if I remove the
tag the page loads fine.

I've sent an email to SBGrid to let them know.

Cheers,
  Thomas

On Mon, Jul 8, 2019 at 4:53 AM Jared Sampson <jar...@gm...> wrote:
>
> Hi PyMOLers -
>
> I'm currently not able to access the label page on PyMOL Wiki, which prints out a string of PHP errors. Weirdly, it appears to be specific to that page, as others (off the top of my head, I visited load and save) appear to be working fine.
>
> Can anyone else confirm this?  If so, I wonder if it can be fixed by an admin.
>
> Cheers,
> Jared
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe