RE: [PyMOL] sphere sizes

[Warren DeLano]

John,

You're not doing anything wrong -- there's just a little confusion
here about how settings work: they're global for an object or for the whole
system.  The current value is what is always used.  To get different sphere
sizes, use the alter command to change the vdw radii of the atoms for which
you wish to change the radii, followed by a rebuild command.

   alter selection, expression
   rebuild

For example:

   alter name ca, vdw=vdw*0.5
   alter resi 200, vdw=vdw*2.0
   rebuild

Cheers,
Warren

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 John Berrisford
 Sent: Thursday, February 26, 2004 2:13 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] sphere sizes
 
 I am trying to create a picture containing a metal ion and 
 water molecules.  The problem that I am having is that I wish 
 to display them both as spheres, but of different sizes. 
 Pymol (version 0.93 and 0.95 beta 11 ) seems to only use the 
 last sphere size command i.e. set sphere_scale, 0.1 in the 
 script and effectively ignore any previous sphere_scale command.
 
 Am I doing something wrong and there is another, better way 
 of doing this, for example linking the size command to an object?
 
 I have been so far unable to work out how to do this.
 
 Thanks
 
 John
 
 --
 John Berrisford
 Department of Molecular Biology and Biotechnology University 
 of Sheffield
 
 email: j.berrisf...@sheffield.ac.uk
 
 
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[PyMOL] sphere sizes

[John Berrisford]

I am trying to create a picture containing a metal ion and water molecules.  The
problem that I am having is that I wish to display them both as spheres, but of
different sizes. Pymol (version 0.93 and 0.95 beta 11 ) seems to only use the
last sphere size command i.e. set sphere_scale, 0.1 in the script and
effectively ignore any previous sphere_scale command.

Am I doing something wrong and there is another, better way of doing this, for
example linking the size command to an object?

I have been so far unable to work out how to do this.

Thanks

John

-- 
John Berrisford
Department of Molecular Biology and Biotechnology
University of Sheffield

email: j.berrisf...@sheffield.ac.uk