VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Nov 06 1999 - 00:17:28 CST

> I'm trying to get the rmsd between
> 2 pdb files. When I load in 2 pdb files,
> do fit-> two molecules -> heavy atoms
> and click on the 2 molecules, vmd crashes.
> I'm running vmd 1.3 on LINUX 2.3.12 redhat 5.2. Is this fixed
> in a later version of vmd?

I was not previously aware that anyone has had trouble
with the rmsd fit on Linux, yours is the first report of
this problem. Although I have not reinstalled VMD 1.3 to
test this yet, I'll do this and see if I'm able to get our
box to crash vmd as you describe. To my knowledge there
shouldn't be anything wrong with rmsd fit on any of the
platforms. But, read on:

> Also vmd crashes when
> I do 'set sel1 [atomselect 0 "backbone"]'
> in an attempt to later find the rmsd.

This should definitely not crash, if it does then there's
certainly something wrong.

Would it be possible for you to make your molecule file(s) available
for us to download to see if the problem is specific to your data and
also to make sure that if there is a bug, that its fixed in VMD 1.4??
We really appreciate having people's files, it makes tracking down
problems in the code much easier.

I plan on releasing VMD 1.4 beta 2 this weekend or on Monday,
you should probably give it a try if you've got the time. It
has a number of improvements over 1.3.
(beta 2 is why I've been slow to respond to email, I've been
 thrashing through building and testing the 12 binary distributions
 we are making)

Let me know if you can make your files available..

Thanks for using VMD!
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
Theoretical Biophysics Group   Email: johns_at_ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
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