pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Bondurant,

I really like the merging of the graphic beauty of pymol with the detailed
depictions of reduce and probe.  I have a method that is a bit clunky for
doing what you ask, but I don't know if it ever made it to the mainstream
in MolProbity.  The caveat of wanting to work with a ligand makes it a bit
harder to explain so my apologies in advance if things aren't 100% clear
but here goes....

1. Make sure you have a reduce definition file for your ligand.  If the
ligand had been deposited in the PDB before ~2012 then the
reduce_wwPDB_het_dict file found (
http://kinemage.biochem.duke.edu/software/reduce.php)  should have it,
otherwise here's an example:

RESIDUE   ACP      11
CONECT      P      4 O1   O2   O3   O4
CONECT      O1     1 P
CONECT      O2     1 P
CONECT      O3     1 P
CONECT      O4     2 P    C1
CONECT      C1     3 O4   O5   C2
CONECT      O5     1 C1
CONECT      C2     4 C1  HC1  HC2  HC3
CONECT     HCH1    1 C2
CONECT     HCH2    1 C2
CONECT     HCH3    1 C2
END
HET    ACP              8
HETNAM     ACP ACETYL PHOSPHATE
FORMUL      ACP    C2 H3 O5 P1 2-

2. download the reduce and probe executables also from
http://kinemage.biochem.duke.edu/

3.  run reduce make sure to use the -DB flag to input your ligand dictionary

4. run probe with a command something like:
probe -both "chaina 88 (ATOM_OG1 | ATOM_HG1)" "chainx 1" CheY_A88T_AcP_H.pdb
Where chain A in this case is the protein and the hydroxyl of Thr 88 is the
only relevant interacting group with chain X the ligand.

5. convert the probe output to a python script to render the cgo objects in
pymol using the attached perl script.  ./probe_to_cgo [input probe dots]
[output pymol cgo]

6. use the run command in pymol to execute the python script and draw the
cgo output.

If this all works the first go then amazing!  If not I can try to help get
things working, but it's been a few years since I last used these tools.

Best of Luck!
-bob



On Fri, Aug 29, 2014 at 10:30 AM, Bondurant <bon...@gm...> wrote:

> Hello community,
> I would like to draw a figure similar to this one
> http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg
> showing the clashes between a potential ligand and the protein. The only
> way i know how to do this in pymol is using the show_bumps plugin, but i
> don't really like the "red disks" format.
> Could anyone tell me how i could easily draw something similar to those
> red spikes from the example to represent the clashes in pymol or any other
> program? I'm able to do it using molprobity and kinemage, but there's no
> much possibilities for editing and to get it in printing quality.
> Thanks
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear All:

Help!
Re-installing Pymol 1.7.0.5 after uninstalling failed with the following 
error:
"Pymol 64 bit setup:    Object already exists."
When I pressed OK, the following message appeared:
"Setup wizard ended prematurely because of an error.  To install at a 
later time run setup wizard again.""
I ran it again with the same result.

Downloading version 1.7.2.1 had the same result.  Deleting the Pymol 
subdirectory in Program Files didn't help. Neither did trying to install 
the 32 bit version.

Has anyone an idea that may solve the problem?

Thanks,
Peter

-- 
Peter C. Kahn, Ph.D.
Professor of Biochemistry
Department of Biochemistry & Microbiology
Rutgers University
76 Lipman Drive
New Brunswick, NJ 08901

NOTE NEW TELEPHONE NUMBER: 848-932-5618

Telefax:    732-932-8965
Email:      ka...@ae...

Hello,

There's a file at examples/devel/chempy_model02.py that uses get_model()
with the following comment at the bottom.

# Summary: this is portable, safe, but inefficient.  For real-time
visualization
# of coordinate changes, there is a way to do this by passing in an opaque
# C data structure...

Does anyone know what this was referring to or how to achieve this?

Thank you Jared,

Then probably I will just modify the PDB file directly.

Best,
Chen


On Fri, Aug 29, 2014 at 12:56 PM, Sampson, Jared <Jar...@ny...>
wrote:

>  Hi Chen -
>
>  As you guessed, this is commonly done by modifying the B-factor column
> directly.  You can do this with data available to you in PyMOL (e.g.
> distances, charges, and so forth) using alter
> <" rel="nofollow">http://pymolwiki.org/index.php/Alter> and iterate
> <" rel="nofollow">http://pymolwiki.org/index.php/Iterate>  and a few other related
> commands.  There are examples on the wiki to help as well.
>
>  For other types of information, you can modify the B-factor column
> values directly in a text editor or other program.
>
>  In either case, your last step will likely include the spectrum
> <" rel="nofollow">http://pymolwiki.org/index.php/Spectrum> command.
>
>  Good luck!
>
>  Cheers,
> Jared
>
>   --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
>  On Aug 29, 2014, at 12:25 PM, Chen Zhao <che...@GM...> wrote:
>
>   Dear all,
>
>  I am thinking whether it is possible to color a molecule by a specific
> property residue-wise or atom-wise like generally be done on B-factor? This
> property could be provided as numbers in a column. An obvious way might
> just be to change the B-factor column to the user-provided column and
> "color by B-factor". But I am wondering whether there are some direct ways
> of doing this.
>
>  Best,
>  Chen
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/_______________________________________________
> 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 Chen -

As you guessed, this is commonly done by modifying the B-factor column directly.  You can do this with data available to you in PyMOL (e.g. distances, charges, and so forth) using alter<" rel="nofollow">http://pymolwiki.org/index.php/Alter> and iterate<" rel="nofollow">http://pymolwiki.org/index.php/Iterate>  and a few other related commands.  There are examples on the wiki to help as well.

For other types of information, you can modify the B-factor column values directly in a text editor or other program.

In either case, your last step will likely include the spectrum<" rel="nofollow">http://pymolwiki.org/index.php/Spectrum> command.

Good luck!

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Aug 29, 2014, at 12:25 PM, Chen Zhao <che...@GM...<mailto:che...@GM...>> wrote:

Dear all,

I am thinking whether it is possible to color a molecule by a specific property residue-wise or atom-wise like generally be done on B-factor? This property could be provided as numbers in a column. An obvious way might just be to change the B-factor column to the user-provided column and "color by B-factor". But I am wondering whether there are some direct ways of doing this.

Best,
Chen
------------------------------------------------------------------------------
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Dear all,

I am thinking whether it is possible to color a molecule by a specific
property residue-wise or atom-wise like generally be done on B-factor? This
property could be provided as numbers in a column. An obvious way might
just be to change the B-factor column to the user-provided column and
"color by B-factor". But I am wondering whether there are some direct ways
of doing this.

Best,
Chen

Why don't you to modify the show_bump.py file?
You could try playing with the line
cmd.show_as('cgo', name)
and change cgo to, for exemple, dots
and see what happens.

Cheers

On 8/29/14 4:30 PM, Bondurant wrote:
> Hello community,
> I would like to draw a figure similar to this one
> http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg
> showing the clashes between a potential ligand and the protein. The only
> way i know how to do this in pymol is using the show_bumps plugin, but i
> don't really like the "red disks" format.
> Could anyone tell me how i could easily draw something similar to those
> red spikes from the example to represent the clashes in pymol or any
> other program? I'm able to do it using molprobity and kinemage, but
> there's no much possibilities for editing and to get it in printing quality.
> Thanks
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>


-- 
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz							
38027 Grenoble Cedex 1						
France	
_________________________________________________________
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

Hello community,
I would like to draw a figure similar to this one
http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg
showing the clashes between a potential ligand and the protein. The only
way i know how to do this in pymol is using the show_bumps plugin, but i
don't really like the "red disks" format.
Could anyone tell me how i could easily draw something similar to those red
spikes from the example to represent the clashes in pymol or any other
program? I'm able to do it using molprobity and kinemage, but there's no
much possibilities for editing and to get it in printing quality.
Thanks

D'uh!!!

I need to get used to always "ray" before assuming anything.

Sorry for the noise!

-----Original Message-----
From: Justin Lecher [mailto:j.l...@fz...] 
Sent: Tuesday, August 26, 2014 4:24 AM
To: pym...@li...
Subject: Re: [PyMOL] cartoon_transparency issue

On 25/08/14 18:42, Markus Heller wrote:
> Hello,
> 
> Attached is a crop of a figure create with the latest PyMOL under Windoze 7 64 bit.  When setting cartoon_transparency, I get a gray band on the cartoons.  Where does this come from, and how do I get rid of it?
> 
> Thanks and Cheers
> Markus
> 
> Here's my code:
> 
> # reset everything
> delete all
> 
> # white background
> bg_color white
> 
> # show valences
> set valence, 1
> 
> # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1
> 
> # antialias
> set antialias = 1
> 
> # load the PDB files
> 
> load ... example PDB
> 
> # turn on grid mode and set it up
> set grid_mode, 1
> 
> # hide everything
> hide everything
> 
> # select protein
> select prot, polymer
> 
> # color everything
> color white
> 
> # show cartoon ribbon for protein
> show cartoon
> 
> # don't show backbone for cartoons
> set cartoon_side_chain_helper, on
> 
> # keep standard helix, strand, loop representations # other options: cartoon loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic
> 
> # color cartoon white and set transparency set cartoon_color, white set cartoon_transparency, 0.7
> 
> # select residue of interest
> select roi, resi 27+31+34+37+41
> 
> # show sticks for ROIs
> show sticks, roi
> 
> # hide non-polar H
> hide (h. and (e. c extend 1))
> 
> # color ROIs
> color atomic
> color yellow, (name C* and roi)
> 
> # show H-bonds between sidechains and assign to slots dist Hbo-sc, resi 37, resi 41, mode = 2
> 
> # hide alls labels
> hide labels
> 
> # color all dashes green
> set dash_color, green
> 
> # deselect all to avoid little pink squares deselect
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Slashdot TV.  
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> 
> 
> 
> _______________________________________________
> 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 markus,

just raytrace you figure using the "ray" command.

Justin

-- 
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117

Hi Niyaz,

You can install a version of Gromacs yourself. The script detects which
version is active (and installs one if none is found).

Cheers,

Tsjerk


On Thu, Aug 28, 2014 at 2:09 AM, niyaz.sabir <niy...@gm...> wrote:

>  Dear PyMol Users,
>
>
> I am a PyMol-Gromacs plugin (
> http://www.pymolwiki.org/index.php/GROMACS_Plugin) user and find the
> plugin great.
> I used to use Ubuntu 10.04 OS and the plugin did not work on it. I could
> manage to run the plugin only on Ubuntu 12.04 and higher.
> The reason was not the kernel since your soft works nice on Ubuntu 12.04
> with old 2.6.32.64 kernel. The problem is probably in Gromacs version.
> PyMol plugin works with Gromacs 4.5.5 and Gromacs version of Ubuntu Lucid
> is v.4.0.7
> My computer is rather slow, 2.66 GHz, 4 Gb RAM with 1 node processor and I
> would therefore like to keep using Ububntu 10.04 instead of moving to
> Ubuntu 12 -14.
> Is there any possibility to make PyMol Gromacs plugin work on  Ubuntu
> 10.04 ?
> Does anybody know how to ovecome the problem ?
>
> Thank you in advance for your answer,
>
> Sincerely ,
>
> Niyaz Safarov, PhD.
> --------------------------------
> Dept of Biophysics and Molecular Biology,
>
> Baku State University,
>
> Baku, Azerbaijan Republic
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> 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.

Dear Pymol users,

I have encountered a problem while trying to install pymol from the source
code on Centos 7.

I am running the following script for installation:

*****

#!/bin/bash -e

prefix=/home/christos/PROGRAMS/PYMOL/OPEN-SOURCE/pymol
modules=$prefix/modules

python setup.py build install \
    --home=$prefix \
    --install-lib=$modules \
    --install-scripts=$prefix

****

and I get the following error:

*********************************************

python2.7 -o build/lib.linux-x86_64-2.7/pymol/_cmd.so
/usr/bin/ld: skipping incompatible /usr/lib/libGL.so when searching for -lGL
/usr/bin/ld: skipping incompatible
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/../../../libGL.so when searching for
-lGL
/usr/bin/ld: skipping incompatible /lib/libGL.so when searching for -lGL
/usr/bin/ld: skipping incompatible /usr/lib/libGL.so when searching for -lGL
/usr/bin/ld: cannot find -lGL
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1

******************************************

I have been unable to overcome this problem. I think it is related with the
fact that I installed NVIDIA drivers on my system but cannot be sure.

Does anyone have any suggestions regarding the error I am getting?

I have installed all but one dependencies with the command:

 yum install subversion gcc gcc-c++ kernel-devel python-devel tkinter
python-pmw glew-devel freeglut-devel libpng-devel freetype-devel

The package python-pmw was not found so I had to manually install that one.

I also tried to do

yum install pymol

however there was no pymol package available.

Is there a repository for centos 7 that includes pymol?

Thank you for considering my problem,

Christos Deligkaris, PhD
Assistant Professor of Physics, Drury University
900 N Benton Ave, Springfield MO, 65802
Office Phone: (417) 873-7234
www2.drury.edu/christos <" rel="nofollow">http://www2.drury.edu/christos/index.html>
@DeligkarisGroup <" rel="nofollow">https://twitter.com/DeligkarisGroup> +ChristosDeligkaris
<" rel="nofollow">http://google.com/+ChristosDeligkaris>

Dear PyMol Users,


I am a PyMol-Gromacs plugin ( http://www.pymolwiki.org/index.php/GROMACS_Plugin) user and find the plugin great. 
I used to use Ubuntu 10.04 OS and the plugin did not work on it. I could manage to run the plugin only on Ubuntu 12.04 and higher.
The reason was not the kernel since your soft works nice on Ubuntu 12.04 with old 2.6.32.64 kernel. The problem is probably in Gromacs version.
PyMol plugin works with Gromacs 4.5.5 and Gromacs version of Ubuntu Lucid is v.4.0.7
My computer is rather slow, 2.66 GHz, 4 Gb RAM with 1 node processor and I would therefore like to keep using Ububntu 10.04 instead of moving to Ubuntu 12 -14.
Is there any possibility to make PyMol Gromacs plugin work on  Ubuntu 10.04 ?

Does anybody know how to ovecome the problem ?

Thank you in advance for your answer,
  
 Sincerely ,
  
 Niyaz Safarov, PhD.
--------------------------------
Dept of Biophysics and Molecular Biology,
  
 Baku State University,
  
 Baku, Azerbaijan Republic

Hi Matt,

I just double-checked, this was a major refactoring of the dynamic_measures setting which didn't make it into Open-Source PyMOL yet. So if you don't have access to Incentive PyMOL, then please use the workarounds.

Cheers,
  Thomas

On 27 Aug 2014, at 11:25, Matthew Baumgartner <mp...@pi...> wrote:
> Hi,
> I am running version 1.7.2.1 from the svn (revision 4088) and the bug 
> with dynamic_measures persists. Unsetting it as in that link corrects 
> that issue though.
> 
> I can send you my files that find the error if you would like.
> 
> Matt
> 
> On 08/27/2014 11:19 AM, Thomas Holder wrote:
>> Hi Matt,
>> 
>> this was a bug with the dynamic_measures setting. It was fixed in PyMOL 1.7.0. So please upgrade PyMOL or read this old post for workarounds:
>> 
>> http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501...@us.../
>> 
>> Cheers,
>>   Thomas
>> 
>> On 27 Aug 2014, at 10:30, Matthew Baumgartner <mp...@pi...> wrote:
>> 
>>> Hi,
>>> I ran into a bug with the find polar contacts function (distance with
>>> mode=2) today. The problem arises when I was trying to find the hydrogen
>>> bonds between a ligand and a receptor that had been processed with
>>> reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A
>>> bug/feature of reduce is that when it adds hydrogens, it gives all of
>>> the newly added hydrogens a 0 as the atom index in the pdb file.
>>> So what happens is when you try to find the polar contacts between the
>>> ligand and the receptor, it draws a bond between a ligand atom and the
>>> last hydrogen (which happens to be non-polar) which is 12 A away. I'm
>>> guessing it is because pymol is using the atom index from the pdb.
>>> One possible alternative would be to index based on the set of the atom
>>> id, atom name, residue name, chain id, and residue ID, but I don't know
>>> how feasible that is.
>>> 
>>> The work around that I have found is to pass the receptor through babel
>>> after processing with reduce. babel prot.pdb prot2.pdb , which
>>> re-indexes the atom ids.
>>> 
>>> Matt Baumgartner


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi,
I am running version 1.7.2.1 from the svn (revision 4088) and the bug 
with dynamic_measures persists. Unsetting it as in that link corrects 
that issue though.

I can send you my files that find the error if you would like.

Matt

On 08/27/2014 11:19 AM, Thomas Holder wrote:
> Hi Matt,
>
> this was a bug with the dynamic_measures setting. It was fixed in PyMOL 1.7.0. So please upgrade PyMOL or read this old post for workarounds:
>
> http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501...@us.../
>
> Cheers,
>    Thomas
>
> On 27 Aug 2014, at 10:30, Matthew Baumgartner <mp...@pi...> wrote:
>
>> Hi,
>> I ran into a bug with the find polar contacts function (distance with
>> mode=2) today. The problem arises when I was trying to find the hydrogen
>> bonds between a ligand and a receptor that had been processed with
>> reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A
>> bug/feature of reduce is that when it adds hydrogens, it gives all of
>> the newly added hydrogens a 0 as the atom index in the pdb file.
>> So what happens is when you try to find the polar contacts between the
>> ligand and the receptor, it draws a bond between a ligand atom and the
>> last hydrogen (which happens to be non-polar) which is 12 A away. I'm
>> guessing it is because pymol is using the atom index from the pdb.
>> One possible alternative would be to index based on the set of the atom
>> id, atom name, residue name, chain id, and residue ID, but I don't know
>> how feasible that is.
>>
>> The work around that I have found is to pass the receptor through babel
>> after processing with reduce. babel prot.pdb prot2.pdb , which
>> re-indexes the atom ids.
>>
>> Matt Baumgartner

Hi Matt,

this was a bug with the dynamic_measures setting. It was fixed in PyMOL 1.7.0. So please upgrade PyMOL or read this old post for workarounds:

http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501...@us.../

Cheers,
  Thomas

On 27 Aug 2014, at 10:30, Matthew Baumgartner <mp...@pi...> wrote:

> Hi,
> I ran into a bug with the find polar contacts function (distance with 
> mode=2) today. The problem arises when I was trying to find the hydrogen 
> bonds between a ligand and a receptor that had been processed with 
> reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A 
> bug/feature of reduce is that when it adds hydrogens, it gives all of 
> the newly added hydrogens a 0 as the atom index in the pdb file.
> So what happens is when you try to find the polar contacts between the 
> ligand and the receptor, it draws a bond between a ligand atom and the 
> last hydrogen (which happens to be non-polar) which is 12 A away. I'm 
> guessing it is because pymol is using the atom index from the pdb.
> One possible alternative would be to index based on the set of the atom 
> id, atom name, residue name, chain id, and residue ID, but I don't know 
> how feasible that is.
> 
> The work around that I have found is to pass the receptor through babel 
> after processing with reduce. babel prot.pdb prot2.pdb , which 
> re-indexes the atom ids.
> 
> Matt Baumgartner

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi,
I ran into a bug with the find polar contacts function (distance with 
mode=2) today. The problem arises when I was trying to find the hydrogen 
bonds between a ligand and a receptor that had been processed with 
reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A 
bug/feature of reduce is that when it adds hydrogens, it gives all of 
the newly added hydrogens a 0 as the atom index in the pdb file.
So what happens is when you try to find the polar contacts between the 
ligand and the receptor, it draws a bond between a ligand atom and the 
last hydrogen (which happens to be non-polar) which is 12 A away. I'm 
guessing it is because pymol is using the atom index from the pdb.
One possible alternative would be to index based on the set of the atom 
id, atom name, residue name, chain id, and residue ID, but I don't know 
how feasible that is.

The work around that I have found is to pass the receptor through babel 
after processing with reduce. babel prot.pdb prot2.pdb , which 
re-indexes the atom ids.

Matt Baumgartner

-- 

On 27 August 2014 16:10, James Starlight <jms...@gm...> wrote:

> *Q: My structure has multiple chains. Which one will be used for the
> calculation? *
> A: Generally, all of them. Be careful, though. While most chains are
> "legitimate" chains corresponding to subunits of the whole multi-mer (as in
> e.g. hemoglobin), some PDB files use chain identifier "A", "B", etc. to
> denote different models of the same monomer (as in e.g. 2TRX). Make sure
> you supply only the one you want. For NMR structures, *you get a window
> where you can choose which model to use*.
>
>
But still it says you can use only one at a time.


> i guess it indicate that in principle some ensembles are possible as the
> input :) Alternatively do you know any other tools (software) for the
> processing of the ensembles with such options for the analysis?
>
>
No.


> James
>
>
> 2014-08-27 15:05 GMT+02:00 Thomas Evangelidis <te...@gm...>:
>
>
>>
>>
>> On 27 August 2014 15:43, James Starlight <jms...@gm...> wrote:
>>
>>> and than how to quick merged aligned conformers back to the NMR ensemble
>>> including TER record between each model in it?
>>>
>>>
>>> Actually I'm looking for the possibility to load this ensemble to the
>>> http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states
>>> for the titrable residues in case of each model and obtained back ensemble
>>> with the processed conformers.
>>>
>>> I think H++ server processes one structure per job. Where did you find
>> that you can upload an ensemble?
>>
>>
>>>
>>> At this time using such nmr ensemble I've faced with the below error
>>>
>>> FAILURE: Sequence discontinuity occurred between residues 289 and 1 at
>>> the line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
>>>
>>> I don't why this error occurs (I have not this in case of ONE model from
>>> the ensemble)
>>>
>>> James
>>>
>>>
>>> 2014-08-27 13:10 GMT+02:00 Thomas Evangelidis <te...@gm...>:
>>>
>>> split_states <NMR-ensemble object name>
>>>> alignto <1st NMR model name>, method=cealign
>>>>
>>>>
>>>> On 27 August 2014 13:28, James Starlight <jms...@gm...>
>>>> wrote:
>>>>
>>>>> also please tell me how is it possible to include ter record at the
>>>>> end of each model.
>>>>>
>>>>> James
>>>>>
>>>>>
>>>>> 2014-08-27 11:58 GMT+02:00 James Starlight <jms...@gm...>:
>>>>>
>>>>> Dear Pymol users!
>>>>>>
>>>>>> Using below script I can load all pdbs from the work dir into 1
>>>>>> nmr-like object. Could you suggest me how this script could be modified to
>>>>>> make alignment (or it's better structural alignment) of all pdbs against
>>>>>> first loaded pdb file
>>>>>>
>>>>>> from pymol import cmd
>>>>>> import sys,glob
>>>>>>
>>>>>> def get_file_list(files):
>>>>>>   file_list = glob.glob(files)
>>>>>>   return file_list
>>>>>>
>>>>>> def load_models(files,obj,discrete=0):
>>>>>>   """
>>>>>>   load_models <files>, <object>, <discrete=0>
>>>>>>
>>>>>>   loads multiple files (using filename globbing)
>>>>>>   into a single object (e.g. from modelling or NMR).
>>>>>>
>>>>>>   use discrete=1 if you want to color individual states separately
>>>>>>
>>>>>>   e.g. load_models prot_*.pdb, prot
>>>>>>   """
>>>>>>   if type(files) == type('string'):
>>>>>>     file_list = get_file_list(files)
>>>>>>   else:
>>>>>>     file_list = files
>>>>>>
>>>>>>   if file_list:
>>>>>>     file_list.sort()
>>>>>>     for name in file_list:
>>>>>>       cmd.load(name,obj,discrete=discrete)
>>>>>>   else:
>>>>>>     print "No files found for pattern %s" % files
>>>>>>
>>>>>> cmd.extend('load_models',load_models)
>>>>>>
>>>>>>
>>>>>> Many thanks for help,
>>>>>>
>>>>>> James
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Slashdot TV.
>>>>> Video for Nerds.  Stuff that matters.
>>>>> http://tv.slashdot.org/
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list (PyM...@li...)
>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>> Archives:
>>>>> http://www.mail-archive.com/pym...@li...
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ======================================================================
>>>>
>>>> Thomas Evangelidis
>>>>
>>>> PhD student
>>>> University of Athens
>>>> Faculty of Pharmacy
>>>> Department of Pharmaceutical Chemistry
>>>> Panepistimioupoli-Zografou
>>>> 157 71 Athens
>>>> GREECE
>>>>
>>>> email: te...@ph...
>>>>
>>>>           te...@gm...
>>>>
>>>>
>>>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>>>
>>>> ===============================================================
>>>>
>>>> *Physics is the only real science. The rest are just stamp collecting.*
>>>>
>>>> *- Ernest Rutherford*
>>>>
>>>>
>>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>>
>> email: te...@ph...
>>
>>           te...@gm...
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>> ===============================================================
>>
>> *Physics is the only real science. The rest are just stamp collecting.*
>>
>> *- Ernest Rutherford*
>>
>>
>


-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: te...@ph...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/

===============================================================

*Physics is the only real science. The rest are just stamp collecting.*

*- Ernest Rutherford*

*Q: My structure has multiple chains. Which one will be used for the
calculation? *
A: Generally, all of them. Be careful, though. While most chains are
"legitimate" chains corresponding to subunits of the whole multi-mer (as in
e.g. hemoglobin), some PDB files use chain identifier "A", "B", etc. to
denote different models of the same monomer (as in e.g. 2TRX). Make sure
you supply only the one you want. For NMR structures, you get a window
where you can choose which model to use.

i guess it indicate that in principle some ensembles are possible as the
input :) Alternatively do you know any other tools (software) for the
processing of the ensembles with such options for the analysis?

James


2014-08-27 15:05 GMT+02:00 Thomas Evangelidis <te...@gm...>:

>
>
>
> On 27 August 2014 15:43, James Starlight <jms...@gm...> wrote:
>
>> and than how to quick merged aligned conformers back to the NMR ensemble
>> including TER record between each model in it?
>>
>>
>> Actually I'm looking for the possibility to load this ensemble to the
>> http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states
>> for the titrable residues in case of each model and obtained back ensemble
>> with the processed conformers.
>>
>> I think H++ server processes one structure per job. Where did you find
> that you can upload an ensemble?
>
>
>>
>> At this time using such nmr ensemble I've faced with the below error
>>
>> FAILURE: Sequence discontinuity occurred between residues 289 and 1 at
>> the line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
>>
>> I don't why this error occurs (I have not this in case of ONE model from
>> the ensemble)
>>
>> James
>>
>>
>> 2014-08-27 13:10 GMT+02:00 Thomas Evangelidis <te...@gm...>:
>>
>> split_states <NMR-ensemble object name>
>>> alignto <1st NMR model name>, method=cealign
>>>
>>>
>>> On 27 August 2014 13:28, James Starlight <jms...@gm...> wrote:
>>>
>>>> also please tell me how is it possible to include ter record at the end
>>>> of each model.
>>>>
>>>> James
>>>>
>>>>
>>>> 2014-08-27 11:58 GMT+02:00 James Starlight <jms...@gm...>:
>>>>
>>>> Dear Pymol users!
>>>>>
>>>>> Using below script I can load all pdbs from the work dir into 1
>>>>> nmr-like object. Could you suggest me how this script could be modified to
>>>>> make alignment (or it's better structural alignment) of all pdbs against
>>>>> first loaded pdb file
>>>>>
>>>>> from pymol import cmd
>>>>> import sys,glob
>>>>>
>>>>> def get_file_list(files):
>>>>>   file_list = glob.glob(files)
>>>>>   return file_list
>>>>>
>>>>> def load_models(files,obj,discrete=0):
>>>>>   """
>>>>>   load_models <files>, <object>, <discrete=0>
>>>>>
>>>>>   loads multiple files (using filename globbing)
>>>>>   into a single object (e.g. from modelling or NMR).
>>>>>
>>>>>   use discrete=1 if you want to color individual states separately
>>>>>
>>>>>   e.g. load_models prot_*.pdb, prot
>>>>>   """
>>>>>   if type(files) == type('string'):
>>>>>     file_list = get_file_list(files)
>>>>>   else:
>>>>>     file_list = files
>>>>>
>>>>>   if file_list:
>>>>>     file_list.sort()
>>>>>     for name in file_list:
>>>>>       cmd.load(name,obj,discrete=discrete)
>>>>>   else:
>>>>>     print "No files found for pattern %s" % files
>>>>>
>>>>> cmd.extend('load_models',load_models)
>>>>>
>>>>>
>>>>> Many thanks for help,
>>>>>
>>>>> James
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Slashdot TV.
>>>> Video for Nerds.  Stuff that matters.
>>>> http://tv.slashdot.org/
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>>
>>>
>>>
>>>
>>> --
>>>
>>> ======================================================================
>>>
>>> Thomas Evangelidis
>>>
>>> PhD student
>>> University of Athens
>>> Faculty of Pharmacy
>>> Department of Pharmaceutical Chemistry
>>> Panepistimioupoli-Zografou
>>> 157 71 Athens
>>> GREECE
>>>
>>> email: te...@ph...
>>>
>>>           te...@gm...
>>>
>>>
>>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>>
>>> ===============================================================
>>>
>>> *Physics is the only real science. The rest are just stamp collecting.*
>>>
>>> *- Ernest Rutherford*
>>>
>>>
>>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: te...@ph...
>
>           te...@gm...
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> ===============================================================
>
> *Physics is the only real science. The rest are just stamp collecting.*
>
> *- Ernest Rutherford*
>
>

is it working here?
https://www.sendspace.com/file/8i0aqo

James


2014-08-27 14:58 GMT+02:00 Justin Lecher <j.l...@fz...>:

> On 27/08/14 07:56, James Starlight wrote:
> > Hi
> >
> > both of them are present in my ensemble. the problem is not here- if it
> > possible i could upload the ensemble.pdb to some server if someone could
> > check it.
> >
> > James
> >
>
> Hi,
>
> Go for some paste bins or do a gist on github.
>
> Justin
>
>
> --
> Justin Lecher
> Institute of Complex Systems
> ICS-6 Structural Biochemistry
> Research Centre Juelich
> 52425 Juelich, Germany
> phone: +49 2461 61 2117
>
>
>

On 27/08/14 07:56, James Starlight wrote:
> Hi
> 
> both of them are present in my ensemble. the problem is not here- if it
> possible i could upload the ensemble.pdb to some server if someone could
> check it.
> 
> James
> 

Hi,

Go for some paste bins or do a gist on github.

Justin


-- 
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117

Hi

both of them are present in my ensemble. the problem is not here- if it
possible i could upload the ensemble.pdb to some server if someone could
check it.

James


2014-08-27 14:52 GMT+02:00 Justin Lecher <j.l...@fz...>:

> On 27/08/14 07:43, James Starlight wrote:
> > and than how to quick merged aligned conformers back to the NMR ensemble
> > including TER record between each model in it?
> >
> >
>
> Hi James,
>
> in addition you need the "MODEL #" [1] - "ENDMDL" [2] entry.
>
> Justin
>
> 1)
> http://wwpdb.org/documentation/format33/sect9.html#MODEL
>
> 2)
> http://wwpdb.org/documentation/format33/sect9.html#ENDMDL
>
>
>
> --
> Justin Lecher
> Institute of Complex Systems
> ICS-6 Structural Biochemistry
> Research Centre Juelich
> 52425 Juelich, Germany
> phone: +49 2461 61 2117
>
>
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

On 27/08/14 07:43, James Starlight wrote:
> and than how to quick merged aligned conformers back to the NMR ensemble
> including TER record between each model in it?
> 
>

Hi James,

in addition you need the "MODEL #" [1] - "ENDMDL" [2] entry.

Justin

1)
http://wwpdb.org/documentation/format33/sect9.html#MODEL

2)
http://wwpdb.org/documentation/format33/sect9.html#ENDMDL



-- 
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117

and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?


Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states for
the titrable residues in case of each model and obtained back ensemble with
the processed conformers.


At this time using such nmr ensemble I've faced with the below error

FAILURE: Sequence discontinuity occurred between residues 289 and 1 at the
line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N

I don't why this error occurs (I have not this in case of ONE model from
the ensemble)

James


2014-08-27 13:10 GMT+02:00 Thomas Evangelidis <te...@gm...>:

> split_states <NMR-ensemble object name>
> alignto <1st NMR model name>, method=cealign
>
>
> On 27 August 2014 13:28, James Starlight <jms...@gm...> wrote:
>
>> also please tell me how is it possible to include ter record at the end
>> of each model.
>>
>> James
>>
>>
>> 2014-08-27 11:58 GMT+02:00 James Starlight <jms...@gm...>:
>>
>> Dear Pymol users!
>>>
>>> Using below script I can load all pdbs from the work dir into 1 nmr-like
>>> object. Could you suggest me how this script could be modified to make
>>> alignment (or it's better structural alignment) of all pdbs against first
>>> loaded pdb file
>>>
>>> from pymol import cmd
>>> import sys,glob
>>>
>>> def get_file_list(files):
>>>   file_list = glob.glob(files)
>>>   return file_list
>>>
>>> def load_models(files,obj,discrete=0):
>>>   """
>>>   load_models <files>, <object>, <discrete=0>
>>>
>>>   loads multiple files (using filename globbing)
>>>   into a single object (e.g. from modelling or NMR).
>>>
>>>   use discrete=1 if you want to color individual states separately
>>>
>>>   e.g. load_models prot_*.pdb, prot
>>>   """
>>>   if type(files) == type('string'):
>>>     file_list = get_file_list(files)
>>>   else:
>>>     file_list = files
>>>
>>>   if file_list:
>>>     file_list.sort()
>>>     for name in file_list:
>>>       cmd.load(name,obj,discrete=discrete)
>>>   else:
>>>     print "No files found for pattern %s" % files
>>>
>>> cmd.extend('load_models',load_models)
>>>
>>>
>>> Many thanks for help,
>>>
>>> James
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Slashdot TV.
>> Video for Nerds.  Stuff that matters.
>> http://tv.slashdot.org/
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: te...@ph...
>
>           te...@gm...
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> ===============================================================
>
> *Physics is the only real science. The rest are just stamp collecting.*
>
> *- Ernest Rutherford*
>
>

split_states <NMR-ensemble object name>
alignto <1st NMR model name>, method=cealign


On 27 August 2014 13:28, James Starlight <jms...@gm...> wrote:

> also please tell me how is it possible to include ter record at the end of
> each model.
>
> James
>
>
> 2014-08-27 11:58 GMT+02:00 James Starlight <jms...@gm...>:
>
> Dear Pymol users!
>>
>> Using below script I can load all pdbs from the work dir into 1 nmr-like
>> object. Could you suggest me how this script could be modified to make
>> alignment (or it's better structural alignment) of all pdbs against first
>> loaded pdb file
>>
>> from pymol import cmd
>> import sys,glob
>>
>> def get_file_list(files):
>>   file_list = glob.glob(files)
>>   return file_list
>>
>> def load_models(files,obj,discrete=0):
>>   """
>>   load_models <files>, <object>, <discrete=0>
>>
>>   loads multiple files (using filename globbing)
>>   into a single object (e.g. from modelling or NMR).
>>
>>   use discrete=1 if you want to color individual states separately
>>
>>   e.g. load_models prot_*.pdb, prot
>>   """
>>   if type(files) == type('string'):
>>     file_list = get_file_list(files)
>>   else:
>>     file_list = files
>>
>>   if file_list:
>>     file_list.sort()
>>     for name in file_list:
>>       cmd.load(name,obj,discrete=discrete)
>>   else:
>>     print "No files found for pattern %s" % files
>>
>> cmd.extend('load_models',load_models)
>>
>>
>> Many thanks for help,
>>
>> James
>>
>
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: te...@ph...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/

===============================================================

*Physics is the only real science. The rest are just stamp collecting.*

*- Ernest Rutherford*

Hi,

If the linear arrangement is defined as 'biological assembly'
in the PDB file, you can use "Biological Unit" script in
http://www.pymolwiki.org/index.php/BiologicalUnit
to quickly generate it.

Best regards,

Takanori Nakane

On 2014-08-27 11:57, Spencer Bliven wrote:
> Sometimes it is easier to see the overall structure when looking at a
> single unit cell rather than the symmetry mates within a certain
> distance. You might want to try the supercell [3] script. Otherwise I
> tend to generate symmetry mates multiple times and then hide or delete
> the ones that don't match the expected biological assembly.
> 
> -Spencer
> 
> On Fri, Aug 15, 2014 at 9:26 AM, sunyeping <sun...@al...>
> wrote:
> 
>> Dear pymol users,
>> 
>> I want to operate a structure whose crystal structure has one
>> molecule in one asymmetry unit. I try to display its polymer. I
>> loaded the structure and used "generate" command in the pymol GUI
>> interface: A>generate>symmetry mates>4A, and then many copies of
>> this molecure appeared but in a quite disoder pattern. According to
>> the paper that published this structure, it is a polymer arranged in
>> a linear pattern. Could you tell me how can I display this linear
>> polymer? Thanks in advance.
>> 
>> Yeping Sun
>> 
>> Institute of Microbiology, Chinese Academy of Sciences
>> 
>> 
> ------------------------------------------------------------------------------
>> 
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> [1]
>> Archives:
>> http://www.mail-archive.com/pym...@li... [2]
> 
> 
> 
> Links:
> ------
> [1] https://lists.sourceforge.net/lists/listinfo/pymol-users
> [2] http://www.mail-archive.com/pym...@li...
> [3] http://www.pymolwiki.org/index.php/Supercell
> 
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...