RE: [PyMOL] biological unit question

2004-04-05 Thread Warren DeLano 
Todd,

Try MacPyMOL for the full PYMOL effect.  http://delsci.com/macpymol

There is also a new command in the 0.95 series:

   split_states object-name

which will spread a PDB "biological unit" (or any multi-state object --
including SD files) over a series of independent objects.  This makes it
possible to interact with such objects more naturally than with "all_states
= 1".

   load 1c8e.pdb1, 1c8e
   split_states 1c8e
   delete 1c8e
   zoom
   spectrum b
   hide lines
   set cartoon_sampling,3
   show cartoon
   bg_color grey70
   set hash_max, 150
   ray
...
   orient
   zoom complete=1
   ray

image & screen-shot at:

  http://delsci.com/img/1c8e.jpg
  http://delsci.com/img/1c8e-screen.jpg

Note that looking at large systems such as this (255300 atoms) may take some
extra RAM -- 1.5 GB is recommended for this task, and it still takes a dual
2 Ghz G5 85 seconds to render...

Cheers,
Warren


> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Todd Geders
> Sent: Friday, April 02, 2004 10:28 AM
> To: Ann Mullin
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] biological unit question
> 
> 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
> 
> 
> 
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Re: [PyMOL] biological unit question

2004-04-02 Thread 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] biological unit question

2004-04-02 Thread Ann Mullin 

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 to 
access the preferences for PyMOL, the option is greyed out on the file 
menu.  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