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=60max_rows=25style=flatviewmonth=200307viewday=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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