pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Everyone,

I hope that this issue is a relatively simple on to resolve.  Is it =
possible to move cgo text in pymol when a pdb is displayed?  How do I do =
perform this task?  Any help you can provide is always greatly =
appreciated!

Thank you in advanced,

jennifer pfingsten

Hi Tassos,

I found the following article, but haven't tried it on my own:

http://www.pymolwiki.org/index.php/Scene

I hope this helps!

Best regards,

Dirk.

Anastassis Perrakis wrote:
> Dear pymolers -
> 
> One can store 'Scenes' and then switch between them; the algorithm  
> that goes from one scene to each other is very nice.
> 
> Can one ask Pymol to write frames going from one scene to another to  
> png files to make a movie ?
> 
> or does anyone have python code that can render the transitions  
> between views/scenes in a different way ?
> 
> best - tassos
> 
> 
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-- 

****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: 	+41-56-310-4722
Fax: 	+41-56-310-5288
E-mail:	dir...@ps...
http://sb.web.psi.ch
****************************************

Dear pymolers -

One can store 'Scenes' and then switch between them; the algorithm  
that goes from one scene to each other is very nice.

Can one ask Pymol to write frames going from one scene to another to  
png files to make a movie ?

or does anyone have python code that can render the transitions  
between views/scenes in a different way ?

best - tassos

Hi,

I installed pymol 0.99rc6 on Fedora core 6. Pymol works fine except 
that I can not use keyboard to type the commands (it ignored any 
input, I tried to change SCIM setup without success ). Any 
suggestions would be appreciated.

Thank you!

Xiao-Ping

Thanks for the idea Warren! I'd actually be more than happy to get my  
hands dirty in the actual code but I wasn't able to figure out how to  
change coords. I tried changing the coords in the chempy atoms e.g.

for a in cmd.get_model("myprot").atoms[:1]:
	print a.coords
	a.coords[0] += 1
	print a.coords

for a in cmd.get_model("myprot").atoms[:1]:
	print a.coords
	a.coords[0] += 1
	print a.coords

[0.37400001287460327, 0.37400001287460327, -0.95200002193450928]
[1.3740000128746033, 0.37400001287460327, -0.95200002193450928]
[0.37400001287460327, 0.37400001287460327, -0.95200002193450928]
[1.3740000128746033, 0.37400001287460327, -0.95200002193450928]

but the changes don't seem to stick. Is there some other way via the  
python API?

Thanks!

-Will Sheffler
Baker Lab
University of Washington

On Mar 28, 2007, at 6:45 AM, DeLano Scientific wrote:

> Will,
>
> The easiest approach, short of Python programming, is to  
> temporarily load a
> new pdb file with updated coordinates and simply update the  
> existing object
> before deleting the original.
>
> load original.pdb
> unset auto_zoom
>
> # then repeat the following as often as necessary
>
> set suspend_updates
> load updated.pdb
> update original,updated
> delete updated
> unset suspend_updates
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>
>
> I'm interested prototyping some interactive molecular modeling and
> simulation code using pymol. I know one can change the atomic  
> coordinates
> wholesale in simple ways via alter_state (like x=x+1). Is there an  
> efficient
> way to change all coordinates to arbitrary values (like coordinates  
> output
> from a simulation)? I could select each atom and alter_state it's xyz
> values, but I'm hoping there is a better way.
>
> Thanks!
>
> -Will Sheffler
> Baker Lab
> University of Washington
>
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys-and earn cash
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Thanks for the idea Warren! I'd actually be more than happy to get my  
hands dirty in the actual code but I wasn't able to figure out how to  
change coords. I tried changing the coords in the chempy atoms e.g.

for a in cmd.get_model("myprot").atoms[:1]:
	print a.coords
	a.coords[0] += 1
	print a.coords

for a in cmd.get_model("myprot").atoms[:1]:
	print a.coords
	a.coords[0] += 1
	print a.coords

[0.37400001287460327, 0.37400001287460327, -0.95200002193450928]
[1.3740000128746033, 0.37400001287460327, -0.95200002193450928]
[0.37400001287460327, 0.37400001287460327, -0.95200002193450928]
[1.3740000128746033, 0.37400001287460327, -0.95200002193450928]

but the changes don't seem to stick. Is there some other way via the  
python API?

Thanks!

-Will Sheffler
Baker Lab
University of Washington

On Mar 28, 2007, at 6:45 AM, DeLano Scientific wrote:

> Will,
>
> The easiest approach, short of Python programming, is to  
> temporarily load a
> new pdb file with updated coordinates and simply update the  
> existing object
> before deleting the original.
>
> load original.pdb
> unset auto_zoom
>
> # then repeat the following as often as necessary
>
> set suspend_updates
> load updated.pdb
> update original,updated
> delete updated
> unset suspend_updates
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>
>
> I'm interested prototyping some interactive molecular modeling and
> simulation code using pymol. I know one can change the atomic  
> coordinates
> wholesale in simple ways via alter_state (like x=x+1). Is there an  
> efficient
> way to change all coordinates to arbitrary values (like coordinates  
> output
> from a simulation)? I could select each atom and alter_state it's xyz
> values, but I'm hoping there is a better way.
>
> Thanks!
>
> -Will Sheffler
> Baker Lab
> University of Washington
>
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Will,

The easiest approach, short of Python programming, is to temporarily load a
new pdb file with updated coordinates and simply update the existing object
before deleting the original.

load original.pdb
unset auto_zoom

# then repeat the following as often as necessary

set suspend_updates
load updated.pdb
update original,updated
delete updated
unset suspend_updates

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...


I'm interested prototyping some interactive molecular modeling and
simulation code using pymol. I know one can change the atomic coordinates
wholesale in simple ways via alter_state (like x=x+1). Is there an efficient
way to change all coordinates to arbitrary values (like coordinates output
from a simulation)? I could select each atom and alter_state it's xyz
values, but I'm hoping there is a better way. 

Thanks!

-Will Sheffler
Baker Lab
University of Washington

Hi David,

The state sort of refers to the frame or model in case of a
multiframe/multimodel (multistate) system. You don't need to use it
with set, it's optional. Just note that "dash_length" and dash_length
are quite different things.

Best,

Tsjerk

On 3/28/07, David Shin <da...@sc...> wrote:
> This regards to my last post.
>
> I finally got it with:
> PyMOL>set dash_length, 0.1, measure01, 1
>
> and got the message:
> Setting: dash_length set to 0.10000 in object "measure01", state 1.
>
> but was wondering what "state" actually refers too...
>
> ie. previously, I tried:
> PyMOL>set "dash_length", 0.1, measure01
>
> and got the error:
> Error: unknown setting '"dash_length"'.
>
> which is why asked the question before.
>
> Thanks,
> Dave
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi.

I'm interested prototyping some interactive molecular modeling and
simulation code using pymol. I know one can change the atomic coordinates
wholesale in simple ways via alter_state (like x=x+1). Is there an efficient
way to change all coordinates to arbitrary values (like coordinates output
from a simulation)? I could select each atom and alter_state it's xyz
values, but I'm hoping there is a better way.

Thanks!

-Will Sheffler
Baker Lab
University of Washington

This regards to my last post.

I finally got it with:
PyMOL>set dash_length, 0.1, measure01, 1

and got the message:
Setting: dash_length set to 0.10000 in object "measure01", state 1.

but was wondering what "state" actually refers too...

ie. previously, I tried:
PyMOL>set "dash_length", 0.1, measure01

and got the error:
Error: unknown setting '"dash_length"'.

which is why asked the question before.

Thanks,
Dave

Hi -

I have some hydrogen bonds and metal-ligand bonds that we want to look
differently.


On MacPymol
I used:
Wizard>>Measurement to create the bonds

I can manipulate how the look under:
Setting>>Edit All
and changing parameters under the "Dash" settings.

Is there some command line input I can use to say set "Measure01"
differently than "Measure02" objects?

I tried outputting what happens with "Edit All" into a .log file, but the
syntax isn't helping me figure out how to manipulate the setting for
individual objects.

I'm looking for some form of syntax that is applicable to everything under
"Edit All" - but for now, those for dash will do.

Thanks,
Dave

PyMOLers,

I updated CEAlign.  If you're using it, please upgrade; I think you'll like 
the changes:
	* Fixed a scoring bug in my implementation of CEAlign
	* Cleaned up memory leaks
	* Added "alignto" function for quick & easy multiple structure alignments
	* Added BASIC instructions for getting this to work with precompiled PyMOL 
		(see wiki)

CEAlign Home Page:
	http://www.pymolwiki.org/index.php/Cealign

Test Cases for v0.6 (compare to v0.2)
	http://www.pymolwiki.org/index.php/Cealign#Results_From_v0.6

v0.6 Code
	http://www.pymolwiki.org/index.php/Cealign#Version_0.6

As usual, please forward bugs/issues to me, or if it interests the list, here.

Cheers,

-- Jason 

-- 

Jason Vertrees (jav...@ut...)
Doctoral Student
Biophysical, Structural & Computational Biology Program
University of Texas Medical Branch 
Galveston, Texas

http://www.best.utmb.edu/
http://www.pymolwiki.org/

Hi Jonathan,=20

I particularly haven't had to deal with BIOMT records before. Maybe the
discussion in the following link might be of use:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2623.html

Cheers
-RB


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of jonathan
sheehan
Sent: Tuesday, March 27, 2007 10:40 AM
To: pym...@li...
Subject: Re: [PyMOL] dimer

On 3/22/07, Bandaranayake, Rajintha
<Raj...@um...> wrote:
>  symexp sym=3Dpdb,(pdb),4.0  # Creates symmetry partners within 4 A of =

> molecule pdb

Very nice. Is there a way to do this using the BIOMT records?

------------------------------------------------------------------------
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V
_______________________________________________
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PyM...@li...
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On 3/22/07, Bandaranayake, Rajintha <Raj...@um...> wrote:
>  symexp sym=pdb,(pdb),4.0  # Creates symmetry partners within 4 A of molecule pdb

Very nice. Is there a way to do this using the BIOMT records?

Hi everyone,
I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces.
Everything works fine.
My question is:
I have uploaded the structure of protein A and the surface of protein B.
What it shows to me is a "blank" surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, "projecting" potential values of protein's  surface B on the surface of protein A, like having a "negative" of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A.
Am I wrong?

Thank for your answer, in advance,



Gianluigi Caltabiano
Lab of Computational Medicine,
BioStatistic Dept.
UAB, Universitat Autonoma de Barcelona
Spain




	

	
		
___________________________________ 
L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: 
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Hi
  We're about to buy some new workstations for the students, and IT have asked about what graphics performance we need. It's of course possible to get glxgears to print FPS, with the -iacknowledgethatthistoolisnotabenchmark switch, but we're more interested in how pymol behaves:-) Do anyone have a script that prints fps in pymol of various standard models and settings? wire/surface/transperancy etc?

Best Regards
Esben



 
____________________________________________________________________________________
Don't pick lemons.
See all the new 2007 cars at Yahoo! Autos.
http://autos.yahoo.com/new_cars.html 

Hello,

> Can someone else chime in with FC6 experiences?  Is this problem rare,
> common, or universal with that distro?

I have no problem with Pymol 0.99rc6 under FC6.

Regards,
Pascal

Vala,

What do you mean by Calcium Phosphates pymol files? If you mean
structures of calcium phosphate..., try to find them on the web,
searching for pdb files or other formats. Pymol is a molecular
viewer.., it doesn't really come with such files from itself.
Alternatively, since calcium phosphate is fairly simple, you could
build a structure yourself...

Tsjerk

On 3/23/07, Alireza Valanezhad <a.v...@gm...> wrote:
> Dear all,
>
> I need to some kinds of Calcium Phosphates pymol files for my project.
>
> Thanx
> Vala
>
> --
> Alireza Valanezhad
> ------------------------
>  Phd Monbokagakushu Scholarship
> Biomaterials, Dental Science Department
> Kyushu University
> Email: A.v...@Gm...
>            Va...@De...
> Tel: +81-092-642-6347
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Dear all,

I need to some kinds of Calcium Phosphates pymol files for my project.

Thanx
Vala

-- 
Alireza Valanezhad
------------------------
Phd Monbokagakushu Scholarship
Biomaterials, Dental Science Department
Kyushu University
Email: A.v...@Gm...
          Va...@De...
Tel: +81-092-642-6347

Dear PyMol users and authors,

I am working on writing a plug-in for pymol and
I have a question regarding the selection of atoms.

I would like to select through the interactive window
(shift+left-click) atoms which have a specific depth
from the solvent-accessible-surface.

To do so I thought to modify this selection system
in a way that the window created for the selection
has a maximum depth in the space.

Do you have any suggestion?

Thanks,

Giacomo Bastianelli
Ph.D student

I have the same problem on PyMOL 0.99rc6 under FC6. 


>
>Just a quick reminder to everyone:  Please include version numbers when
>reported problems with PyMOL.
>
>Jose,
>
>PyMOL uses GLUT on Linux, so there may be a problem between X11 and GLUT on
>FC6.  It is also possible that there is some permissions issue that is
>preventing unprivileged processes from receiving events inside a GLUT-based
>OpenGL window.
>
>Can someone else chime in with FC6 experiences?  Is this problem rare,
>common, or universal with that distro?
>
>Cheers,
>Warren
>
>--
>DeLano Scientific LLC
>Subscriber Support Services
>mailto:de...@de...
> 
>"Not yet a PyMOL Subscriber, but want to support the project?  Email
>sa...@de... to quote your lab, school, or employer.  Thank you for
>sponsoring this open-source endeavor!" -WLD
> 
>
>> -----Original Message-----
>> From: pym...@li... 
>> [mailto:pym...@li...] On Behalf 
>> Of Jose Casasnovas
>> Sent: Thursday, March 22, 2007 7:08 AM
>> To: pym...@li...
>> Subject: [PyMOL] problems with command line
>> 
>> Runing PyMOL under FC6 I can only type on the command line 
>> when running the program as root.  Users can not type in the 
>> PyMOL GUI.
>> Could you provide any solution?
>> 
>> Thanks in advance.
>> 
>> Jose M Casasnovas
>> 
>> 
>> --------------------------------------------------------------
>> -----------
>> Take Surveys. Earn Cash. Influence the Future of IT Join 
>> SourceForge.net's Techsay panel and you'll get the chance to 
>> share your opinions on IT & business topics through brief 
>> surveys-and earn cash 
>> http://www.techsay.com/default.php?page=join.php&p=sourceforge
>> &CID=DEVDEV
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>-------------------------------------------------------------------------
>Take Surveys. Earn Cash. Influence the Future of IT
>Join SourceForge.net's Techsay panel and you'll get the chance to share your
>opinions on IT & business topics through brief surveys-and earn cash
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>https://lists.sourceforge.net/lists/listinfo/pymol-users
>

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

Yu Kitago

Division of Biological Sciences,
Graduate School of Science,
Hokkaido University

Tel: +81-11-706-3433; Fax: +81-11-706-3433
E-mail: ki...@ca...

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

Hi Lisa,

Easiest would be to click on the 'A' button, select 'generate' and =
select 'symmetry mates'. From there you can select within how many =
Angstroms you want your symm molecules to be displayed. From the =
symmetry related molecules that get displayed you can select the  completes the dimer.

Alternately you could try the following command:

symexp sym=3Dpdb,(pdb),4.0  # Creates symmetry partners within 4 A of =
molecule pdb

Hope this helps.

-RB


-----Original Message-----
From: pym...@li... on behalf of Lisa M =
Jones
Sent: Thu 3/22/2007 5:57 PM
To: pym...@li...
Subject: [PyMOL] dimer
=20
Hi all,
=20
I am trying to open a crystal structure of a dimer but I can only get
the monomer to open.  The pdb file has the symmetry coordinates but I
don't know how to turn them on.  Can anyone help me?

Hi all,
=20
I am trying to open a crystal structure of a dimer but I can only get
the monomer to open.  The pdb file has the symmetry coordinates but I
don't know how to turn them on.  Can anyone help me?

Just a quick reminder to everyone:  Please include version numbers when
reported problems with PyMOL.

Jose,

PyMOL uses GLUT on Linux, so there may be a problem between X11 and GLUT on
FC6.  It is also possible that there is some permissions issue that is
preventing unprivileged processes from receiving events inside a GLUT-based
OpenGL window.

Can someone else chime in with FC6 experiences?  Is this problem rare,
common, or universal with that distro?

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Jose Casasnovas
> Sent: Thursday, March 22, 2007 7:08 AM
> To: pym...@li...
> Subject: [PyMOL] problems with command line
> 
> Runing PyMOL under FC6 I can only type on the command line 
> when running the program as root.  Users can not type in the 
> PyMOL GUI.
> Could you provide any solution?
> 
> Thanks in advance.
> 
> Jose M Casasnovas
> 
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys-and earn cash 
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> &CID=DEVDEV
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users

Dirk,

That setting is for the molecular mesh representation, not maps, and it is
also constrained by other factors.

If you want to supersample maps, first load the map, then issue:

map_double map-name

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Dirk Reinert
> Sent: Wednesday, March 21, 2007 11:15 AM
> To: pym...@li...
> Subject: [PyMOL] min_mesh_spacing
> 
> Dear all,
> 
>    using "set min_mesh_spacing, <number>" does not seem to 
> have any effect on my maps. (Yes, I set this before loading 
> the map and creating the mesh.) Am I missing something? Or is 
> 0.6 the lowest mesh spacing allowed ...
> 
> Thanks for all answers and suggestions,
>    Dirk.
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
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