pymol-users Mailing List for PyMOL Molecular Graphics System

Dear all,

I began to use pymol. I would like to know if one has experience in doing
conformational search using pymol in python or invoking it in unix ?
I am mainly using Mac, so, I would appreciate if you could guide me with
this.

Cheers,
Nik

PDB format dictates that TER records are present at the end of a polymer chain. 
Chain breaks or non-sequential numbering do not introduce TER records.  A TER 
record is required between the polymer and non-polymer chain - even with same 
chain ID. TER records should not be between non-polymers...

Of course, there have been many different flavors of PDB files produced by 
different programs...

http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER

On 11/28/2016 10:31 AM, Spencer Bliven wrote:
> It would be nice to have a setting that adds TER records only where the chain 
> or segi change (as opposed to whenever the residue numbers are 
> non-sequential). I believe that better captures the original intent for 
> terminating polymers. Of course, the real answer is that everyone should 
> switch to mmCIF.
>
> On Mon, Nov 28, 2016 at 4:01 PM, Thomas Holder <tho...@sc... 
> <mailto:tho...@sc...>> wrote:
>
>     Hi Marko and Rui,
>
>     The TER records can also be prevented with "set pdb_use_ter_records, off".
>
>     https://pymolwiki.org/index.php/pdb_use_ter_records
>     <" rel="nofollow">https://pymolwiki.org/index.php/pdb_use_ter_records>
>
>     Cheers,
>       Thomas
>
>     On 28 Nov 2016, at 05:03, Rui Sousa <Rui...@un...
>     <mailto:Rui...@un...>> wrote:
>
>     > Hi Marko,
>     >
>     > For the order of the atoms, check if "retain_order" is set to 1; if not,
>     > use "set retain_order, 1" before importing your PDB file. For the rest
>     > of your problem, what exactly is being changed from the imported PDB
>     > file and the saved one? Apart from the addition of TER, which is a
>     > fairly trivial problem to solve.
>     >
>     > Best regards,
>     >
>     > Rui
>     >
>     > Le 28/11/2016 10:41, Marko Sever a écrit :
>     >> Hello everybody,
>     >>
>     >> I'm working with a protein-protein complex and am fixing some stuff.
>     >>
>     >> When I save the fixed complex as a pdb the PDB format is not the same
>     as it was in the imported pdb files (there it was the same as the CHARMM
>     default pdb format).
>     >>
>     >> In the saved pdb it changed the line position of atoms in the pdb file.
>     Residues are ok but atoms in a given residue are mixed up. It also added
>     addition TER's which I had to manually delete.
>     >>
>     >> So how would I specify the output PDB format to be the same as in the
>     original imported pdbs (before manipulation), so same as CHARMM pdb format.
>     >>
>     >> Please help,
>     >>
>     >> Marko
>
>     --
>     Thomas Holder
>     PyMOL Principal Developer
>     Schrödinger, Inc.
>
>
>     ------------------------------------------------------------------------------
>     _______________________________________________
>     PyMOL-users mailing list (PyM...@li...
>     <mailto:PyM...@li...>)
>     Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>     <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>     Archives: http://www.mail-archive.com/pym...@li...
>     <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

It would be nice to have a setting that adds TER records only where the
chain or segi change (as opposed to whenever the residue numbers are
non-sequential). I believe that better captures the original intent for
terminating polymers. Of course, the real answer is that everyone should
switch to mmCIF.

On Mon, Nov 28, 2016 at 4:01 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Marko and Rui,
>
> The TER records can also be prevented with "set pdb_use_ter_records, off".
>
> https://pymolwiki.org/index.php/pdb_use_ter_records
>
> Cheers,
>   Thomas
>
> On 28 Nov 2016, at 05:03, Rui Sousa <Rui...@un...> wrote:
>
> > Hi Marko,
> >
> > For the order of the atoms, check if "retain_order" is set to 1; if not,
> > use "set retain_order, 1" before importing your PDB file. For the rest
> > of your problem, what exactly is being changed from the imported PDB
> > file and the saved one? Apart from the addition of TER, which is a
> > fairly trivial problem to solve.
> >
> > Best regards,
> >
> > Rui
> >
> > Le 28/11/2016 10:41, Marko Sever a écrit :
> >> Hello everybody,
> >>
> >> I'm working with a protein-protein complex and am fixing some stuff.
> >>
> >> When I save the fixed complex as a pdb the PDB format is not the same
> as it was in the imported pdb files (there it was the same as the CHARMM
> default pdb format).
> >>
> >> In the saved pdb it changed the line position of atoms in the pdb file.
> Residues are ok but atoms in a given residue are mixed up. It also added
> addition TER's which I had to manually delete.
> >>
> >> So how would I specify the output PDB format to be the same as in the
> original imported pdbs (before manipulation), so same as CHARMM pdb format.
> >>
> >> Please help,
> >>
> >> Marko
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Marko and Rui,

The TER records can also be prevented with "set pdb_use_ter_records, off".

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

Cheers,
  Thomas

On 28 Nov 2016, at 05:03, Rui Sousa <Rui...@un...> wrote:

> Hi Marko,
> 
> For the order of the atoms, check if "retain_order" is set to 1; if not, 
> use "set retain_order, 1" before importing your PDB file. For the rest 
> of your problem, what exactly is being changed from the imported PDB 
> file and the saved one? Apart from the addition of TER, which is a 
> fairly trivial problem to solve.
> 
> Best regards,
> 
> Rui
> 
> Le 28/11/2016 10:41, Marko Sever a écrit :
>> Hello everybody,
>> 
>> I'm working with a protein-protein complex and am fixing some stuff.
>> 
>> When I save the fixed complex as a pdb the PDB format is not the same as it was in the imported pdb files (there it was the same as the CHARMM default pdb format).
>> 
>> In the saved pdb it changed the line position of atoms in the pdb file. Residues are ok but atoms in a given residue are mixed up. It also added addition TER's which I had to manually delete.
>> 
>> So how would I specify the output PDB format to be the same as in the original imported pdbs (before manipulation), so same as CHARMM pdb format.
>> 
>> Please help,
>> 
>> Marko

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,

Yeah, this one catches me off-guard now and again. Chain labels were made
case-sensitive, as assemblies sometimes become so large that more than 26
labels are required. So, you'll probably need to specify 'chain A' in stead
of 'chain a'.

Hope it helps,

Tsjerk

On Mon, Nov 28, 2016 at 3:13 PM, <Reu...@mh...> wrote:

> Dear Tsjerk,
>
> thank you for your reply.
>
>
>
> The very simple script
>
>
>
> bg_color white
>
> load 2j6o-coot-0.pdb
>
>
>
> works fine as the pdb-file is loaded and displayed as line model (as it
> should) with v.1.8.40.
>
>
>
> Adding the line
>
>
>
> select SH3, resi 2-58 and chain a
>
>
>
> yields  a selection called SH3 (as expected) but this does not contain any
> atoms. As I already wrote, the same script (plus lots of additional lines)
> works flawlessly using v1.8.07.
>
>
>
> I will be happy about any possibly helpful suggestion.
>
>
>
> Best
>
> Thomas
>
>
>
>
>
>
>
> *Von:* Tsjerk Wassenaar [mailto:ts...@gm...]
> *Gesendet:* Donnerstag, 24. November 2016 15:36
> *An:* Reubold, Thomas Dr.
> *Cc:* pymol-users
> *Betreff:* Re: [PyMOL] Scripts don't work any longer after upgrade to
> v1.8.4
>
>
>
> Hi Thomas,
>
>
>
> Can you give more information? What is in the script? Is something written
> in the terminal?
>
> FWIW, I have not encountered problems, and certainly not with selections.
> My guess is that the script breaks before getting to the selection.
>
>
>
> Cheers,
>
>
>
> Tsjerk
>
>
>
> On Thu, Nov 24, 2016 at 2:13 PM, <Reu...@mh...> wrote:
>
> Hello all,
>
>
>
> after installation of Pymol v.1.8.4 on our Linux system, scripts that used
> to work fine with v.1.8.0.7 do not work anymore. Even a simple selection
> does not work.
>
> Is this a known problem? If so, is there a way to fix it?
>
> Any help is greatly appreciated.
>
>
>
> Best,
>
> Thomas
>
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
>
>
> --
>
> Tsjerk A. Wassenaar, Ph.D.
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Hi Marko,

For the order of the atoms, check if "retain_order" is set to 1; if not, 
use "set retain_order, 1" before importing your PDB file. For the rest 
of your problem, what exactly is being changed from the imported PDB 
file and the saved one? Apart from the addition of TER, which is a 
fairly trivial problem to solve.

Best regards,

Rui

Le 28/11/2016 10:41, Marko Sever a écrit :
> Hello everybody,
>
> I'm working with a protein-protein complex and am fixing some stuff.
>
> When I save the fixed complex as a pdb the PDB format is not the same as it was in the imported pdb files (there it was the same as the CHARMM default pdb format).
>
> In the saved pdb it changed the line position of atoms in the pdb file. Residues are ok but atoms in a given residue are mixed up. It also added addition TER's which I had to manually delete.
>
> So how would I specify the output PDB format to be the same as in the original imported pdbs (before manipulation), so same as CHARMM pdb format.
>
> Please help,
>
> Marko
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hello everybody,

I'm working with a protein-protein complex and am fixing some stuff.

When I save the fixed complex as a pdb the PDB format is not the same as it was in the imported pdb files (there it was the same as the CHARMM default pdb format).

In the saved pdb it changed the line position of atoms in the pdb file. Residues are ok but atoms in a given residue are mixed up. It also added addition TER's which I had to manually delete.

So how would I specify the output PDB format to be the same as in the original imported pdbs (before manipulation), so same as CHARMM pdb format.

Please help,

Marko

Dear all, 
I am trying to install pymol on my centos 6 system from source following the guide on the pymolwiki ("https://pymolwiki.org/index.php/Linux_Install)". The installation process seemed to be successful but when I initialized pymol, I got the following error: 
import _tkinter # If this fails your Python may not be configured for Tk
ImportError: libtk8.6.so: cannot open shared object file: No such file or directory.
How could I solve the problem?
I'll appreciate any help!
Best regards.
Yeping Sun

Adding to my previous answer, keep in mind that PyMOL, by default, uses 
the camera to interpret the vector. Therefore, if you change your window 
view, this vector will change. You can specify the "camera" variable (by 
using, for example "translate [100,0,0], obj2, camera=0") so that the 
vector is relative to the model's axes instead.

Le 25/11/2016 12:37, Rui Sousa a écrit :
> Hello Sajeewa,
>
> The translate command uses angström as a unit. Therefore, if you want 
> to translate obj2 by 10 nm, you should use "translate [100,0,0]" 
> instead of "translate [10,0,0]".
>
> Best regards,
>
> Rui
>
> Le 25/11/2016 12:04, Sajeewa Pemasinghe a écrit :
>> Hello everyone,
>>
>> I have a linear molecule (obj1)  which I have duplicated (obj2). I 
>> want to move obj2 (which is currently 100% overlapped with obj1) with 
>> respect to obj1 along the x axis by 10 nm. Can I achieve this by
>>
>> translate [10,0,0] , obj2
>>
>> I don't know what the distance units are in the vector used in 
>> translate command.
>>
>> Is there a much better way of achieving what I have described?
>>
>> Best regards,
>>
>> Sajeewa
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:http://www.mail-archive.com/pym...@li...
>

Hello Sajeewa,

The translate command uses angström as a unit. Therefore, if you want to 
translate obj2 by 10 nm, you should use "translate [100,0,0]" instead of 
"translate [10,0,0]".

Best regards,

Rui

Le 25/11/2016 12:04, Sajeewa Pemasinghe a écrit :
> Hello everyone,
>
> I have a linear molecule (obj1)  which I have duplicated (obj2). I 
> want to move obj2 (which is currently 100% overlapped with obj1) with 
> respect to obj1 along the x axis by 10 nm. Can I achieve this by
>
> translate [10,0,0] , obj2
>
> I don't know what the distance units are in the vector used in 
> translate command.
>
> Is there a much better way of achieving what I have described?
>
> Best regards,
>
> Sajeewa
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hello everyone,

I have a linear molecule (obj1)  which I have duplicated (obj2). I want to
move obj2 (which is currently 100% overlapped with obj1) with respect to
obj1 along the x axis by 10 nm. Can I achieve this by

translate [10,0,0] , obj2

I don't know what the distance units are in the vector used in translate
command.

Is there a much better way of achieving what I have described?

Best regards,

Sajeewa

Hi Thomas,

Can you give more information? What is in the script? Is something written
in the terminal?
FWIW, I have not encountered problems, and certainly not with selections.
My guess is that the script breaks before getting to the selection.

Cheers,

Tsjerk

On Thu, Nov 24, 2016 at 2:13 PM, <Reu...@mh...> wrote:

> Hello all,
>
>
>
> after installation of Pymol v.1.8.4 on our Linux system, scripts that used
> to work fine with v.1.8.0.7 do not work anymore. Even a simple selection
> does not work.
>
> Is this a known problem? If so, is there a way to fix it?
>
> Any help is greatly appreciated.
>
>
>
> Best,
>
> Thomas
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Hello all,

after installation of Pymol v.1.8.4 on our Linux system, scripts that used to work fine with v.1.8.0.7 do not work anymore. Even a simple selection does not work.
Is this a known problem? If so, is there a way to fix it?
Any help is greatly appreciated.

Best,
Thomas

Hi Yuxing,

We have released Incentive PyMOL 1.8.4.1, which fixes the ribbon coloring issue.

Cheers,
  Thomas

On 21 Nov 2016, at 15:57, Thomas Holder <tho...@sc...> wrote:

> Hi Yuxing,
> 
> Thanks for reporting this. Yes it's a bug, luckily with a simple fix. We will provide a bugfix release soon.
> 
> Cheers,
>  Thomas
> 
> On 21 Nov 2016, at 15:12, Yuxing Liao <Yux...@UT...> wrote:
> 
>> Hello All,
>> 
>> I just updated Pymol from 1.8.0 to the latest 1.8.4. But I noticed when the structure is rendered in ribbon and you try to color part of it, the behavior changed at the boundaries. Instead of beginning and ending at the middle of the bonds like before, now the colors start and end at joints (actually colors one residue prior to the N-terminal of the selection). Is this a bug?
>> 
>> Thanks.
>> 
>> Yuxing
>> 
>> UT Southwestern
>> 
>> Medical Center
>> 
>> The future of medicine, today.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Yuxing,

Thanks for reporting this. Yes it's a bug, luckily with a simple fix. We will provide a bugfix release soon.

Cheers,
  Thomas

On 21 Nov 2016, at 15:12, Yuxing Liao <Yux...@UT...> wrote:

> Hello All,
>  
> I just updated Pymol from 1.8.0 to the latest 1.8.4. But I noticed when the structure is rendered in ribbon and you try to color part of it, the behavior changed at the boundaries. Instead of beginning and ending at the middle of the bonds like before, now the colors start and end at joints (actually colors one residue prior to the N-terminal of the selection). Is this a bug?
>  
> Thanks.
>  
> Yuxing
> 
> UT Southwestern
> 
> Medical Center
> 
> The future of medicine, today.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello All,

I just updated Pymol from 1.8.0 to the latest 1.8.4. But I noticed when the structure is rendered in ribbon and you try to color part of it, the behavior changed at the boundaries. Instead of beginning and ending at the middle of the bonds like before, now the colors start and end at joints (actually colors one residue prior to the N-terminal of the selection). Is this a bug?

Thanks.

Yuxing

________________________________

UT Southwestern


Medical Center



The future of medicine, today.

Dear pymol users,
I would like to calculate vander waals interaction of a patricular
residue in a pdb. kindly tell me how to do it?

Thanks in advance
Surya
Graduate student
India.

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The lab has state-of-the-art equipment and facilities. We have dedicated
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Interested candidates can send an e-mail to ani...@ni... with a
CV and a summary of previous research experience and future interests.

Hello Everyone,

Is there any method to fast locate the keyframes when I making a movie by pymol? You know when the movie have too many frames, it is very difficult to remember which frames are the keyframes and the movie panel doesn't show it clearly.

Best regards,
Lei Zhen

==========================================
Name: Lei Zhen
Address:
Num.501, College of Chemistry,
Beijing Normal University
No. 19, XinJieKouWai St., HaiDian District,
Beijing 100875, P. R. China
Email: le...@ma...<mailto:le...@ma...> / thu...@ou...<mailto:thu...@ou...>
Tel: (+86) 010-58806002
==========================================

Hi, Lei Zen
The example script in https://pymolwiki.org/index.php/MovieSchool_5 shows smooth changes in camera and object transformation, color and representation change in discrete jumps.

PyMOL does not automatically interpolate colors or transparency, only transformations. Mostly, smooth color changes are used in morphs - when you create a morph, you create a multistate object, which you can color in a range of colors using the spectrum_states.py  script. (https://pymolwiki.org/index.php/Spectrum_states). 
With "State Sweep" you rifle through the different states in your object.

Example:

viewport 500,500
bg_color white
load http://www.rcsb.org/pdb/files//1Q21.pdb
load http://www.rcsb.org/pdb/files//1QRA.pdb
align 1Q21, 1QRA, cycles=0, object=aln
morph QQQ, 1Q21, 1QRA
hide all
show ribbon
#download scripts from https://pymolwiki.org/index.php/Spectrum_states
run py_scripts/spectrum_states.py 
spectrum_states QQQ, ribbon, red purpleblue blue

Run this with Movie: Program: State Sweep: ¼ Speed: No Pause

Alternatively you can split the animations into enough key frames that the discrete jumps in color or transparency (to fade objects in or out)  appear smooth to the observer.

Best regards
Annemarie Honegger


Message: 1
Date: Fri, 18 Nov 2016 02:37:50 +0000
From: ? ? <thu...@ou...>
Subject: [PyMOL] a pymol problem: cannot transit smoothly between
representations in animation
To: "pym...@li..."
<pym...@li...>
Message-ID:
<SIX...@SI...>

Content-Type: text/plain; charset="us-ascii"

Dear all,

I come across the same problem as the link below, which is that my movie made by pymol cannot transit between different representations smoothly. It cannot transit smoothly either when I click the scene buttons. It seems very simple in MovieSchool5 on pymolwiki website. I don't know why it doesn't work for both of us. Thank you very much!
The link is here.
https://sourceforge.net/p/pymol/mailman/message/35074780/
The command I use is here.
[cid:image001.png@01D24185.0450DDB0]

Best regards,
Lei Zhen
==========================================
Name: Lei Zhen
Address:
Num.501, College of Chemistry,
Beijing Normal University
No. 19, XinJieKouWai St., HaiDian District,
Beijing 100875, P. R. China
Email: le...@ma...<mailto:le...@ma...> / thu...@ou...<mailto:thu...@ou...>
Tel: (+86) 010-58806002
==========================================





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End of PyMOL-users Digest, Vol 126, Issue 2
*******************************************

Dear all,

I come across the same problem as the link below, which is that my movie made by pymol cannot transit between different representations smoothly. It cannot transit smoothly either when I click the scene buttons. It seems very simple in MovieSchool5 on pymolwiki website. I don't know why it doesn't work for both of us. Thank you very much!
The link is here.
https://sourceforge.net/p/pymol/mailman/message/35074780/
The command I use is here.
[cid:image001.png@01D24185.0450DDB0]

Best regards,
Lei Zhen
==========================================
Name: Lei Zhen
Address:
Num.501, College of Chemistry,
Beijing Normal University
No. 19, XinJieKouWai St., HaiDian District,
Beijing 100875, P. R. China
Email: le...@ma...<mailto:le...@ma...> / thu...@ou...<mailto:thu...@ou...>
Tel: (+86) 010-58806002
==========================================

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


> On Nov 14, 2016, at 3:04 PM, Subha K <sub...@gm...> wrote:
> 
> Hi There,
> 
> Just wondering if there is a way to have the same order of atoms (with that of the initial loaded file) while saving a pdb file with pymol?
> 
> I came across an old post on this [https://sourceforge.net/p/pymol/mailman/message/7561093/ <" rel="nofollow">https://sourceforge.net/p/pymol/mailman/message/7561093/>] and not sure if there is a direct way now to do this.
> 
> Thanks and Best Regards,
> Subha
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Great!

Thanks heaps.

Subha

On Mon, Nov 14, 2016 at 1:06 PM, David Hall <li...@co...> wrote:

> https://pymolwiki.org/index.php/Retain_order
>
>
> On Nov 14, 2016, at 3:04 PM, Subha K <sub...@gm...> wrote:
>
> Hi There,
>
> Just wondering if there is a way to have the same order of atoms (with
> that of the initial loaded file) while saving a pdb file with pymol?
>
> I came across an old post on this [https://sourceforge.net/p/
> pymol/mailman/message/7561093/] and not sure if there is a direct way now
> to do this.
>
> Thanks and Best Regards,
> Subha
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>
>

Hi There,

Just wondering if there is a way to have the same order of atoms (with that
of the initial loaded file) while saving a pdb file with pymol?

I came across an old post on this [
https://sourceforge.net/p/pymol/mailman/message/7561093/] and not sure if
there is a direct way now to do this.

Thanks and Best Regards,
Subha