pymol-users Mailing List for PyMOL Molecular Graphics System

Dear PyMol users!


I have a set of conformations extracted from the MD trajectory (on the
equal time-steps). After loading of all that pdb's into pymol (each
conformer= separate pdb file) I want to sort that structures based on the
RMSD relative to the reference conformer (e.g step0.pdb ) in the selected
range (e.g select and sort only structures with RMSD = 0.5 to the 0.pdb. So
if I have 100 conformers I want that pymol select only 5 structures with
rmsd (measured by TMalign plugin for instance) to reference equal to 0.5,
1, 1.5, 2.0, 2.5 and 3.0 Angstroms, respectively).

Does it possible to make such sorting ?


James

Hi Jianghai,

by default PyMOL does a distance based bonding (basically when the VDW
radii of two atoms overlap, they get connected). To prevent that, you
need two settings:

# before saving the correctly bonded but distorted structure
set pdb_conect_all

# before loading
set connect_mode, 1

http://pymolwiki.org/index.php/connect_mode

Cheers,
  Thomas

Jianghai Zhu wrote, On 04/30/13 02:39:
> Hi,
> 
> In my trajectory movie, there are some minor distortions of some of
> the residues, but the sticks presentation in pymol seems fine.
> However, after I loaded the trajectory pdb file use discrete=1, extra
> bonds would be shown in sticks in those slightly distorted residues.
> Is there is way to avoid those extra bonds?  Thanks a lot.
> 
> --Jianghai

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi,

In my trajectory movie, there are some minor distortions of some of the residues, but the sticks presentation in pymol seems fine.  However, after I loaded the trajectory pdb file use discrete=1, extra bonds would be shown in sticks in those slightly distorted residues.  Is there is way to avoid those extra bonds?  Thanks a lot.

--Jianghai

Sounds like a permissions issue. Without more info, I'm not sure what 
your problem might be specifically, but this is how I install pymol on a 
central server that is shared via NFS as /usr/local/xtal:

 1. copy pymol-1.5.0.x directory into desired shared location, e.g.,
    /usr/local/xtal. I do this as a regular user, not as root, but root
    *should* work OK, too if you follow the remaining directions.
 2. Assign group permissions to the pymol-1.5.0.x directory, e.g., chown
    -R username:users pymol-1.5.0.x. Allowed users should be a part of
    the "users" group. This will allow directory access for non-you or
    non-root users.
 3. Change permissions of the directory (if not already set) to 755,
    e.g. chmod 755 pymol-1.5.0.x. I think this is OK already, but you
    should check.
 4. Run the script setup.sh in the pymol directory to generate the pymol
    startup command. I do this as the installation user under my username.
 5. Put a link to the "pymol" startup command in /usr/local/xtal, e.g.
    ln -s ./pymol-1.5.0.x/pymol. My pymol link has 777 permissions by
    default.
 6. Ensure that /usr/local/xtal is mounted by all users and in
    everyone's path.

This allows me to serve pymol to all users on all workstations by 
installing it once.


_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rro...@co...

On 4/29/2013 12:12 AM, John Bruning wrote:
> Hello,
>
> I have installed pymol (v1.5) as root.  When I am logged in as root 
> pymol launches fine with the pymol command.  In the same directory as 
> not root, any other user, I get the following error message:
>
> /usr/local/bin/pymol: line 14: 
> /usr/local/src/pymol/setup/ext/bin/python: No such file or directory
> /usr/local/bin/pymol: line 14: exec: 
> /usr/local/src/pymol/setup/ext/bin/python: cannot execute: No such 
> file or directory
>
> Any ideas on what's wrong?
>
> Thanks,
> John
>
>
> ------------------------------------------------------------------------------
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Hello,

I have installed pymol (v1.5) as root.  When I am logged in as root pymol launches fine with the pymol command.  In the same directory as not root, any other user, I get the following error message:

/usr/local/bin/pymol: line 14: /usr/local/src/pymol/setup/ext/bin/python: No such file or directory
/usr/local/bin/pymol: line 14: exec: /usr/local/src/pymol/setup/ext/bin/python: cannot execute: No such file or directory

Any ideas on what's wrong?

Thanks,
John

I am trying to run pymol on a notebook (olivetti 550) under Ubuntu 12.04.
The notebook has the SIS 771/671 graphic chip.
The PyMOL screen flickers including the internal gui. I manage to install
the drivers from here
https://github.com/hellnest/xf86-video-sismedia-0.9.1and get the
correct resolution but PyMOL is still flickering. I try ubuntu
2d and ubuntu 3D. Any idea of how to fix this?
Thanks.

Hi Thomas,

I'm running into issues with color compatibility between 1.6 and
earlier versions when opening pses
(a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
Setting-Error: type read mismatch (color) 6
Setting-Error: type read mismatch (color) 663
Setting-Error: type read mismatch (color) 664
(b) background color disparity:
saved in 1.5 with black background; opens in 1.6 with a white background
saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
background

These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
others who would like to beta test can use devel:languages:python repo
in openSUSE:
https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython

-David


On Sun, Mar 24, 2013 at 6:02 AM, Thomas Holder
<tho...@sc...> wrote:
> Dear PyMOL users,
>
> The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering.
>
> Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website:
>
>   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>
> As always, we welcome bug reports and positive feedback.
>
> Cheers,
>
> - The PyMOL Team at Schrödinger
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
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My PyMOL 1.5.0.5 works fine in Windows 8 (64 bits).

Try the following:
- Press Windows Key + Q
- This should open the search apps thingy, type pymol
- It should show all PyMOL shortcuts, try the "PyMOL + Tcl-Tk GUI + Console"
- Does PyMOL still refuses to open? Did you get any error message?

On 20/03/2013 03:11, Thomas Holder wrote:
> Hi Nina Marie,
>
> I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5
> runs fine on Windows 8.
>
> Cheers,
>    Thomas
>
> Wolf, Nina Marie wrote, On 03/19/13 21:11:
>> Hi,
>>
>> I recently upgraded my computer to windows 8. Since then, pymol will not
>> open. Is the latest version of pymol incompatible with windows 8? Or is
>> there something I can do to get it working on my computer?

Hi Mehmet,

secondary structure is not a per-state property unless the object has
discrete states. Just write out the multi-state file and load it in
again as discrete:

PyMOL> save yourmorph.pdb, yourmorph, state=0
PyMOL> delete yourmorph
PyMOL> load yourmorph.pdb, discrete=1
PyMOL> dss

There was almost the same question two days ago (Subject: SS in a
trajectory).

Cheers,
  Thomas

vapour wrote, On 04/26/13 17:05:
> Hi,
> 
> I am trying to generate a movie which shows a conformational change
> of my protein. In there, I have one helix unwinding completely and loses
> its helicity. When I do morpheasy, the secondary structure of this helix
> from the starting conformation is still preserved and not converted into
> the loop conformation at the end of the movie. How can I depict this
> change of secondary structure with the morpheasy?
> 
> Cheers,
> mehmet

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Yarrow,

set_bond stick_transparency, 0.5, myObj

Cheers,

-- Jason

On Fri, Apr 26, 2013 at 11:03 AM, Yarrow Madrona <ama...@uc...> wrote:
>
> Hi,
>
> I have previously been able to do a "fake" fade on surface transparency by
> doing the following:
> where "testout" is an object in pymol.
>
> mdo 449: set transparency, 1, testout
> mdo 550: show surface, testout
> mdo 551: set transparency, 0.7, testout
> mdo 552: set transparency, 0.6, testout
> mdo 553: set transparency, 0.5, testout
> mdo 554: set transparency, 0.4, testout
> mdo 555: set transparency, 0.3, testout
> mdo 556: set transparency, 0.3, testout
> mdo 557: set transparency, 0.1, testout
> mdo 558: set transparency, 0, testout
>
>
> The surface will slowly come to life between frames 449 and 558. However,
> if I try doing this with
> "set stick_transparency", nothing happens. I have tried to do this using
> scenes, however the object simply disappears instead of fading. I would
> love some help on this. I am interested in python scripting as well as I
> know a little python but not sure how to implement it in pymol. Thanks!
>
>
> -------------
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
> ------------------------------------------------------------------------------
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> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
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-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,

I have previously been able to do a "fake" fade on surface transparency by
doing the following:
where "testout" is an object in pymol.

mdo 449: set transparency, 1, testout
mdo 550: show surface, testout
mdo 551: set transparency, 0.7, testout
mdo 552: set transparency, 0.6, testout
mdo 553: set transparency, 0.5, testout
mdo 554: set transparency, 0.4, testout
mdo 555: set transparency, 0.3, testout
mdo 556: set transparency, 0.3, testout
mdo 557: set transparency, 0.1, testout
mdo 558: set transparency, 0, testout


The surface will slowly come to life between frames 449 and 558. However,
if I try doing this with
"set stick_transparency", nothing happens. I have tried to do this using
scenes, however the object simply disappears instead of fading. I would
love some help on this. I am interested in python scripting as well as I
know a little python but not sure how to implement it in pymol. Thanks!


-------------
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

Hi,

I am trying to generate a movie which shows a conformational change of my protein. In there, I have one helix unwinding completely and loses its helicity. When I do morpheasy, the secondary structure of this helix from the starting conformation is still preserved and not converted into the loop conformation at the end of the movie. How can I depict this change of secondary structure with the morpheasy?

Cheers,

mehmet

Greetings,

I am delighted to announce that the 2013 PyMOL Open Source Fellowship
program is now accepting applications. Due to the success of the
program, we have two open spots this year.

Application instructions and deadlines for the 2013 PyMOL Open Source
Fellowship have been posted here http://pymol.org/fellowship.
Interested applicants, please review the instructions before applying.

The application deadline is July 1, 2013.

Good luck!

Cheers,

-- Jason

--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Thomas,

actually I used very routine way. Firstly I've  extract conformers of
protein-ligand complexes from the trajectory. Than I've loaded it into
pymol and visualize possible interactions. Than I've selected most
representative conformers and loaded it separately into pose view to obtain
2D maps. I understand that its very routine but I had not any other
alternatives.

By the way during usage of the g_hbond with the below flags

g_hbond -f fitted.trr -s complex.gro -n index.ndx  -hbm ./hb/hbmap.xpm
-life ./hb/hblife.xvg

In the index file I've specified ligand and protein as two groups.  should
I define second group more accurately ( e.g only possible amino acids from
the ligand binding pocket) ?
I've forced with the problem of the interpretation of the hbmap. As I
understood that could be used for the monitoring of the h-bond occurring
and breaking between protein and ligand during MD run. How it could be
visualize to observe particular amino-acids on the first (protein) group
which contribute to H-bonds ?

James

2013/4/24 Thomas Evangelidis <te...@gm...>

>
>
>
>
>
>> As I understood fconv can be used for the split several mol2 (or pdb)
>> files which was placed in 1 model to the several pdb files, doesnt it ?
>>
>> fconv can do miracles :) check it out !
>
> fconv -h
>
>
>
>> In past I forced with some problems with  g_hbond. Is there any other way
>> to monitor h bonds along the trajectory (e.g in vmd) ?
>>
>>
> In contrast, I encountered problems with the H-bonds VMD plugin, that's
> why I resorted to g_hbond. Beware that g_hbonds will count the frequencies
> of salt-bridges too.
>
>
>> PoseView is used as the separate software or web server
>> http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze
>> polar interactions both in pymol as well as via pose view).
>>
>>
> If you find a way to draw the most important protein-ligand interactions
> throughout the trajectory with PoseView, then I would be very interested to
> know how.
>
>
>>
>> James
>>
>> 2013/4/24 Thomas Evangelidis <te...@gm...>
>>
>>>
>>> I want to examine protein-ligand interactions observed in the md
>>>> trajectory using Pymol.
>>>>
>>>> For such task I have 100 snapshots of the protein-ligand complex which
>>>> I've loaded into the pymol. Now I want to extract from all snapshots 100
>>>> ligands as the separate 100 objects and save it in the mol2. Actually I can
>>>> do such task in the simplest way extracting all ligands in one object but I
>>>> need as a result 100 mol2 files. Could someone show me example of some
>>>> script which could do such tasks?
>>>>
>>>>
>>> Save all ligands in a multi-mol mol2 file and then split if with fconv
>>> -s.
>>>
>>> http://pc1664.pharmazie.uni-marburg.de/download/fconv
>>>
>>>
>>>
>>>> Also I'll be very thankful if someone can provide me with some tool
>>>> which can be used for investigation of the ligand dynamics along MD
>>>> trajectory ( in particular I want to visualize all binding poses and define
>>>> all polar contacts along trajectory). For such task I've being used pymol
>>>> as well as pose view loading snapshots to that programs but that way is not
>>>> appropriate for analyzing of the ensembles of the binding poses obtained
>>>> from md run.
>>>>
>>>>
>>> I usually monitor H-bonds with g_hbond from GROMACS Tools and
>>> Salt-Bridges with the respective VMD plugin. Then I make a table with
>>> frequences of each polar interaction, pick up a frame that contains as many
>>> important interactions as possible, load it in PyMOL and draw dotted lines
>>> between the interacting atoms.
>>>
>>> PS: I didn't know about PoseView plugin, it seems to be a very useful
>>> addition to PyMOL :)
>>>
>>> Thomas
>>>
>>>
>
>
> --
>
> ======================================================================
>
> 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/
>
>
>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
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> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
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> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,

On Wed, 2013-04-24 10:31  EDT,  Jianghai Zhu <jz...@id...> wrote:

> Hi,
> 
> I have a trajectory file, in which two short helices would merge into one
> long helix.  However, when I play the trajectory in Pymol as cartoon, the
> long helix would still be shown as two helices with a loop in between.
> Is there a way to force Pymol to show a long helix for a specific range
> of frames in a trajectory? Thanks a lot.

When you load the trajectory, use the discrete flag to have PyMOL computer
the secondary structure for each state .

load trajectory.pdb, discrete=1

I'm assuming you are loading a multi-model .PDB file as the trajectory.  If
you are using the load_traj command to load an AMBER trajectory, there is
no similar option.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

If none suggests a solution in PyMOL ten use sscache.tcl script in VMD to
update the SS at every frame.

Thomas

On 24 April 2013 17:31, Jianghai Zhu <jz...@id...> wrote:

> Hi,
>
> I have a trajectory file, in which two short helices would merge into one
> long helix.  However, when I play the trajectory in Pymol as cartoon, the
> long helix would still be shown as two helices with a loop in between.  Is
> there a way to force Pymol to show a long helix for a specific range of
> frames in a trajectory? Thanks a lot.
>
> --Jianghai
>
>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
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> 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/

Where I can find documentation about the exact meaning of all the settings
related to the sculpt function? In particular what the "sculpt_field_mask"
setting does?

I am trying to sculpt the sidechaiin of a particular residue while
protecting the rest of the structure. Which are the bet parameters to try
to move the sidechain while avoiding clashes/bumps?

Thanks.

> As I understood fconv can be used for the split several mol2 (or pdb)
> files which was placed in 1 model to the several pdb files, doesnt it ?
>
> fconv can do miracles :) check it out !

fconv -h



> In past I forced with some problems with  g_hbond. Is there any other way
> to monitor h bonds along the trajectory (e.g in vmd) ?
>
>
In contrast, I encountered problems with the H-bonds VMD plugin, that's why
I resorted to g_hbond. Beware that g_hbonds will count the frequencies of
salt-bridges too.


> PoseView is used as the separate software or web server
> http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar
> interactions both in pymol as well as via pose view).
>
>
If you find a way to draw the most important protein-ligand interactions
throughout the trajectory with PoseView, then I would be very interested to
know how.


>
> James
>
> 2013/4/24 Thomas Evangelidis <te...@gm...>
>
>>
>> I want to examine protein-ligand interactions observed in the md
>>> trajectory using Pymol.
>>>
>>> For such task I have 100 snapshots of the protein-ligand complex which
>>> I've loaded into the pymol. Now I want to extract from all snapshots 100
>>> ligands as the separate 100 objects and save it in the mol2. Actually I can
>>> do such task in the simplest way extracting all ligands in one object but I
>>> need as a result 100 mol2 files. Could someone show me example of some
>>> script which could do such tasks?
>>>
>>>
>> Save all ligands in a multi-mol mol2 file and then split if with fconv -s.
>>
>> http://pc1664.pharmazie.uni-marburg.de/download/fconv
>>
>>
>>
>>> Also I'll be very thankful if someone can provide me with some tool
>>> which can be used for investigation of the ligand dynamics along MD
>>> trajectory ( in particular I want to visualize all binding poses and define
>>> all polar contacts along trajectory). For such task I've being used pymol
>>> as well as pose view loading snapshots to that programs but that way is not
>>> appropriate for analyzing of the ensembles of the binding poses obtained
>>> from md run.
>>>
>>>
>> I usually monitor H-bonds with g_hbond from GROMACS Tools and
>> Salt-Bridges with the respective VMD plugin. Then I make a table with
>> frequences of each polar interaction, pick up a frame that contains as many
>> important interactions as possible, load it in PyMOL and draw dotted lines
>> between the interacting atoms.
>>
>> PS: I didn't know about PoseView plugin, it seems to be a very useful
>> addition to PyMOL :)
>>
>> Thomas
>>
>>


-- 

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

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/

Thomas, thanks for help!


As I understood fconv can be used for the split several mol2 (or pdb) files
which was placed in 1 model to the several pdb files, doesnt it ?

In past I forced with some problems with  g_hbond. Is there any other way
to monitor h bonds along the trajectory (e.g in vmd) ?

PoseView is used as the separate software or web server
http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar
interactions both in pymol as well as via pose view).


James

2013/4/24 Thomas Evangelidis <te...@gm...>

>
> I want to examine protein-ligand interactions observed in the md
>> trajectory using Pymol.
>>
>> For such task I have 100 snapshots of the protein-ligand complex which
>> I've loaded into the pymol. Now I want to extract from all snapshots 100
>> ligands as the separate 100 objects and save it in the mol2. Actually I can
>> do such task in the simplest way extracting all ligands in one object but I
>> need as a result 100 mol2 files. Could someone show me example of some
>> script which could do such tasks?
>>
>>
> Save all ligands in a multi-mol mol2 file and then split if with fconv -s.
>
> http://pc1664.pharmazie.uni-marburg.de/download/fconv
>
>
>
>> Also I'll be very thankful if someone can provide me with some tool which
>> can be used for investigation of the ligand dynamics along MD trajectory (
>> in particular I want to visualize all binding poses and define all polar
>> contacts along trajectory). For such task I've being used pymol as well as
>> pose view loading snapshots to that programs but that way is not
>> appropriate for analyzing of the ensembles of the binding poses obtained
>> from md run.
>>
>>
> I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges
> with the respective VMD plugin. Then I make a table with frequences of each
> polar interaction, pick up a frame that contains as many important
> interactions as possible, load it in PyMOL and draw dotted lines between
> the interacting atoms.
>
> PS: I didn't know about PoseView plugin, it seems to be a very useful
> addition to PyMOL :)
>
> Thomas
>
> --
>
> ======================================================================
>
> 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/
>
>
>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
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> I want to examine protein-ligand interactions observed in the md
> trajectory using Pymol.
>
> For such task I have 100 snapshots of the protein-ligand complex which
> I've loaded into the pymol. Now I want to extract from all snapshots 100
> ligands as the separate 100 objects and save it in the mol2. Actually I can
> do such task in the simplest way extracting all ligands in one object but I
> need as a result 100 mol2 files. Could someone show me example of some
> script which could do such tasks?
>
>
Save all ligands in a multi-mol mol2 file and then split if with fconv -s.

http://pc1664.pharmazie.uni-marburg.de/download/fconv



> Also I'll be very thankful if someone can provide me with some tool which
> can be used for investigation of the ligand dynamics along MD trajectory (
> in particular I want to visualize all binding poses and define all polar
> contacts along trajectory). For such task I've being used pymol as well as
> pose view loading snapshots to that programs but that way is not
> appropriate for analyzing of the ensembles of the binding poses obtained
> from md run.
>
>
I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges
with the respective VMD plugin. Then I make a table with frequences of each
polar interaction, pick up a frame that contains as many important
interactions as possible, load it in PyMOL and draw dotted lines between
the interacting atoms.

PS: I didn't know about PoseView plugin, it seems to be a very useful
addition to PyMOL :)

Thomas

-- 

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

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/

Hi,

I have a trajectory file, in which two short helices would merge into one long helix.  However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between.  Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot.

--Jianghai

Dear Pymol users!


I want to examine protein-ligand interactions observed in the md trajectory
using Pymol.

For such task I have 100 snapshots of the protein-ligand complex which I've
loaded into the pymol. Now I want to extract from all snapshots 100 ligands
as the separate 100 objects and save it in the mol2. Actually I can do such
task in the simplest way extracting all ligands in one object but I need as
a result 100 mol2 files. Could someone show me example of some script which
could do such tasks?

Also I'll be very thankful if someone can provide me with some tool which
can be used for investigation of the ligand dynamics along MD trajectory (
in particular I want to visualize all binding poses and define all polar
contacts along trajectory). For such task I've being used pymol as well as
pose view loading snapshots to that programs but that way is not
appropriate for analyzing of the ensembles of the binding poses obtained
from md run.


Thanks for help,


James

Hi Gianluigi,

that surface is a CGO object, so you need:

set cgo_transparency, value, object

Hope that helps.

Cheers,
  Thomas

Gianluigi Caltabiano wrote, On 04/22/13 18:49:
> Hi all,
> 
> I often use  VASCo surfaces and I am experiencing a strange behaviour on
> transparency settings as VASCo surfaces do not "respond" to:
> set transparency, value, object 
> Not from the command line, not from the plugin itself. Pymol's surfaces
> get transparent but not the object corresponding to VASCo surface.
> I am not sure but I would say it worked to me before. 
> I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid).
>
> Am I missing something? 
> 
> thanks and regards
> 
> Gianluigi

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi all,

I often use  VASCo surfaces and I am experiencing a strange behaviour on transparency settings as VASCo surfaces do not "respond" to:
set transparency, value, object 
Not from the command line, not from the plugin itself. Pymol's surfaces get transparent but not the object corresponding to VASCo surface.
I am not sure but I would say it worked to me before. 
I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid).


Am I missing something? 

thanks and regards

Gianluigi

Thanks, valence guess was the key :-)

This makes sense, valence/bond assignment is run once the PDB is loaded, but unfortunately fails with the alternate conformations. Removing the alternate conformation doesnt update the bond information, making the save/reload of the structure or valence guess nescessary before the h_add.

Cheers
Esben