[Chimera-users] occupancy with pdb trajectory

Andrea C. Vaiana vaiana at lanl.gov
Wed Dec 5 10:18:07 PST 2007

Hi Eric,

Thanks for the prompt reply. Yes, my pdb is a single file with multiple 
MODEL records. The numbers on the records are consecutive, so I guess 
that's not the problem. My original tpr + trr files are a total of ~25M 
(do you think your email can handle it?). The pdb file was >100M but 
I've tried on a smaller one (with only the first 4 frames of the run) 
and get the same error message. I guess email can handle the small pdb 
file (1M zipped), I will send this in a separate email. Let me know 
if/how I can send you the tpr/trr files.


Eric Pettersen wrote:
> Hi Andrea,
> I _believe_ this indicates that your frames aren't consecutively 
> numbered.  Is your PDB input a single file with multiple MODEL 
> records.  If so, are the numbers on these MODEL records 
> consecutive? Chimera should probably handle non-consecutive numbering 
> (at least when there's a regular "stride") but it doesn't yet.
> I'd also be interested in looking at your tpr/trr problem if you could 
> get the files to me.  How big are they?
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu


Andrea C. Vaiana
Theoretical Biology and Biophysics
Mail stop K710, T-10
Los Alamos, NM 87545
Los Alamos National Laboratory

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