[Chimera-users] fit in map and multimodel pdbs

Martin Lawrence lawrence at chemistry.montana.edu
Thu Oct 6 16:26:00 PDT 2016

Dear Chimera Users,

I have a pdb file for an entire virus (biological assembly) that I can read
into Chimera just fine, as either a multimodel PDB with 60 different
models, or as a PDB lacking model and endmdl cards, but with the atom
number of the multi-model pdb preserved.  The model is placed very close to
the density for the virus in a tomogram.  When I use the fit in map
command, the single model pdb moves nicely by a couple of nm and a few
degrees into the tomogram density.  For the multimodel map I must first use
the combine command in the model panel to combine the 60 differernt models,
but that then also moves nicely into the density.  However, in both cases,
when I try to write out the slightly rotated/translated coordinates to a
PDB file, I wind up with a semi-corrupted PDB file containing **** in many
locations, especially for the last half of the file. Since the virus is
pseudo T=31 with 18 chains in the viral asu, the pdb model has more than 2
million atoms and 1048 chains; the chains obviously cannot be uniquely
identified with a single letter, the atom numbers exceed the the allowed
format, and residues are renumbered and then also exceed the allowed format.

I can fix this by hand to some extent, and could write a jiffy to put it
back into the multiple model format, but feel like there is a more elegant
solution to this problem already embedded in Chimera.  Preferably one that
will allow high throughput down the road.  Any advice would be appreciated!


Martin Lawrence
Department of Chemistry and Biochemistry
Montana State University
Bozeman, MT 59717
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20161006/3b65de19/attachment.html>

More information about the Chimera-users mailing list