VMD-L Mailing List

From: Marc Baaden (baaden_at_smplinux.de)
Date: Wed Oct 30 2002 - 05:33:26 CST

Hi John,

thanks for your answer. In fact this is not really what I was looking
for. But I realize that my question was ill-defined. In fact the only
thing I really want/need is to set the viewpoint in a similar fashion
for every coordinate set loaded. The "problem" is that as I load each
coordinate set seperately, there is no reference structure to fit or
compare to.

So I was looking for a simple general definition, like: look at the
protein such that its geometrical centre is in the centre of the screen
and that residue X is pointing towards you.

I am trying to translate this into "VMD language", and that's where
I would need some assistance. I guess I have to simply set the viewpoints
with some magically calculated matrices.

johns_at_ks.uiuc.edu said:
>> Hi Marc,
>> It sounds like what you want to do could be done by doing a best-fit
>> alignment on a subset of the atoms. There's an example of how do
>> this in the VMD User's Guide:
>> http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node185.html

Concerning the "proper lighting", usually the default view in VMD is
nicely lit, if you render the scene. But if you change the viewpoint,
you might get shadows/unlit areas that are not so nice. So the question
was, how do I re-create, once my viewpoint is chosen, the kind of default
lighting with respect to that position.

>> I'm not sure what you're second question about "proper lighting" is
>> referring to, so I'll wait to answer that until you determine if the
>> best-fit alignment feature above does in fact solve your problem.

I hope I outlined my questions in a better way, if not feel free to
ask for more details.

Thanks,
  Marc 

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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