From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Thu Oct 13 2005 - 13:17:42 CDT

Hi Guys,

Can anyone tell me why I might be getting 'failed to set coordinate' and
'poorly guessed coordinates' warnings when reading a pdb? I examined the
structure and found nothing visibly wrong. These were just warnings, not
errors -- still it would be nice to know what's up.

Sam

reading residues from pdb file inputp.pdb extracted 185 residues from pdb
file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
reading coordinates from pdb file inputp.pdb for segment U
Warning: failed to set coordinate for atom O1 PHE:185 U
Warning: failed to set coordinate for atom O2 PHE:185 U
Info: guessing coordinates for 1495 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 MET:1 U
Warning: poorly guessed coordinate for atom HT2 MET:1 U
Warning: poorly guessed coordinate for atom HT3 MET:1 U
Warning: poorly guessed coordinate for atom OT1 PHE:185 U
Warning: poorly guessed coordinate for atom OT2 PHE:185 U

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Jerry Parks
Sent: Thursday, October 13, 2005 11:22 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Interpolation in internal space

How difficult would it be to generate a linear interpolation from one
conformation to another in internal coordinates and then write out the
coordinate snapshots? Such a script would be very useful to me. Sometimes
cartesian interpolations just don't make physical sense.

Thanks,
Jerry Parks

-----------------------------------------------------------------------
Hi,
  If I understand correctly, what you're asking for is a script
that will linearly interpolate the atom coordinates between two
configurations of the same molecule? If I've misunderstood and
you actually have more than two sets of coordinates (a trajectory for
example)
then you can use the Extensions->Visualization->Movie Maker tool to
make trajectory animations of your simulation. If you indeed are
asking for a script that does linear interpolation of atom coordinates,
I don't have such a script handy but it would be easy to write if
that's what you're actually after.

  John

On Wed, Oct 12, 2005 at 01:58:55PM -0400, Mingliang Tan wrote:
> Dear all,
>
> I would like to know how to show a movie from one static configuration
> (pdb file available) of a protein to another (pdb file available too),
> i.e., is there any way to have a movie showing the intermediate
> structures in VMD?
>
> Thank you very much in advance,
>
> Mingliang

-- 
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