[Chimera-users] problems with your PDB file

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 19 09:27:51 PST 2016


Hi Karthak,
The file you attached only has one structure, so you wouldn’t use MD Movie to view it anyway.  MD Movie is for trajectories of multiple structures (conformations) of the same set of atoms.  I can open it as a single structure using the main File… Open, but not in MD Movie because it is only one structure.  For an example of a single PDB file with multiple structures, see 1G1P in the Protein DataBank:
http://www.rcsb.org/pdb/explore/explore.do?structureId=1g1p

I do not get the error message you report. However, maybe this is not a Chimera question but a file-editing question.  You would have to use a text editor to add END lines (if you need them, I can’t tell) or to add missing atoms or residues to your PDB file. If you want to view a trajectory in MD Movie, however, your file would need to have multiple conformations separated by MODEL and ENDMDL lines as in 1G1P.
Best,
Elaine 
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Dec 19, 2016, at 7:43 AM, Kartheek <kartheek.p at research.iiit.ac.in> wrote:
> 
> Hi UCSF CHIMERA users,
> I am trying to make a movie in chimera using MD movie and pdb option. However I have been stumbled with the following error "Residue 256.C not in first model on line 20792 of /tmp/tmpvr4a2t.pdb". I do not have any end records, how can I rectify the error ??
> 
> -- 
> Sincerely,
> P.Kartheek,
> Research Scholar,
> IIIT-H, Hyderabad,
> INDIA.<15.pdb>



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