Hi Andrea, It turns out that not all functions of MD Movie (such as occupancy calculation) were able to handle trajectories where the first coordinate set was numbered as zero -- as was the case with your file where the first MODEL was zero. I have fixed the code now and it should be available tomorrow from the "Daily Builds" link on the Chimera home page (check the date on the build to make sure the build worked -- the date on tomorrow's build should be Dec 5 since it will build this evening). If you want to do something before then your options are: 1) delete MODEL zero from your file 2) renumber the MODELs in your file 3) Change zero to the highest model number + 1 4) I can send you the changes to the MD Movie module (let me know) --Eric P.S. My mailer should be able to handle the tpr/trr combo. Give it a whirl. If it fails, let me know -- there are other transfer options. On Dec 5, 2007, at 10:18 AM, Andrea C. Vaiana wrote:
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.
Andrea
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
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Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory