Re: [PyMOL] biological unit question

[Todd Geders]

Command line equivalent is the following:

set all_states,1

On Fri, 2004-04-02 at 11:38, Ann Mullin wrote:
> Hello,
> 
> I am also interested in being able to display an entire virus capsid. 
> 
> Ny new question regards Todd's reply to check Movie->Show All States.
> 
> I run Native PyMOL for MacOSX on a G5, and I have never been able
> toaccess the preferences for PyMOL, the option is greyed out on the
> filemenu.  So I am not sure where or how to get the show all states
> option.
> 
> Thanks for the help this list has provided.
> 
> Ann
> 
> 
> Ann Mullin
> Research Scientist
> Cell and Molecular Biology Dept.
> Tulane University
> New Orleans, LA 70118-5698
> 504-865-6742 (Ph)
> 504-865-6785 (FAX)
> amul...@tulane.edu

[PyMOL] "Outline" cartoon representation

[Todd Geders]

Hello all,

We'd like to render some cartoon representations of protein structures
in a manner similar to the style of Jane Richardson.  Basically white,
opaque surfaces (no reflections) with black outlines at each of the
edges.  

Here's a link to give you an idea what we're looking for (Figure 1b-c):
http://www.nature.com/nsmb/journal/v7/n8/fig_tab/nsb0800_624_F1.html

Any suggestions on how to do this using PyMOL?

~Todd

RE: [PyMOL] electrostatic surface

[Todd Geders]

Hello all,

Here is a simple script that automates the electrostatic potential
surface generation using Gromacs, MEAD, and Pymol for visualization. 
It's exclusively based off of the post by Esben Peter Friis:
http://sourceforge.net/mailarchive/forum.php?forum_id=60&max_rows=25&style=flat&viewmonth=200307&viewday=9

It requires you to massage your pdb file a bit, but it gets the job
done.  Please glance at the comments in the script to see what I mean.

Script:
http://expert.ics.purdue.edu/~geders/utilities/pymol_electrostatic_surface.sh

Screenshot:
http://expert.ics.purdue.edu/~geders/utilities/pymol_electrostatic_surface.png

~Todd

On Tue, 2003-12-16 at 16:04, Warren L. DeLano wrote:
> Ruslan,
> 
> PyMOL can't yet calculate the electrostatic surface, but it
> can
> display the potential as output by Grasp, Delphi, MEAD, or Zap.
> 
> Cheers,
> Warren
> 
> 
> --
> mailto:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax   (650)-593-4020
> 
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> > ad...@lists.sourceforge.net] On Behalf Of Sanishvili, Ruslan
> > Sent: Tuesday, December 16, 2003 8:29 AM
> > To: Warren L. DeLano; pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] electrostatic surface
> >
> > Hi all,
> > Inexplicably, I haven't been following the PyMol news lately. Does
> it
> > now calculate and display the electrostatic fields/surfaces of
> proteins
> > (a la GRASP, or similar)? If it does, starting from which version?
> > Thanks,
> > Nukri
> >
> >
> > Ruslan Sanishvili (Nukri), Ph.D.
> >
> > GM/CA-CAT, Bld. 436, D007
> > Biosciences Division, ANL
> > 9700 S. Cass Ave.
> > Argonne, IL 60439
> >
> > Tel: (630)252-0665
> > Fax: (630)252-0667
> > rsanishv...@anl.gov
> >
> >
> >
> >
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