[Chimera-users] occupancy with pdb trajectory

Eric Pettersen pett at cgl.ucsf.edu
Wed Dec 5 12:10:58 PST 2007

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)


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

More information about the Chimera-users mailing list