[Chimera-users] fit in map and multimodel pdbs

Tom Goddard goddard at sonic.net
Fri Oct 7 12:37:32 PDT 2016

Hi Martin,

  The PDB file format can only handle 100,000 atoms and 62 chains for each model.  So the solution is to keep the virus caspsid subunits as separate models, and then save the 60 models in a single PDB file.  To do this you fit all 60 models as one rigid unit.  There is no need to combine them into a single model for fitting.  If you are using the fitmap command simply do something like

	fitmap #1-60 #0

If you are using the Fit Map dialog choose to fit “selected atoms” and select all 60 models with command select #1-60.  When you save the 60 models using File / Save PDB… use the dialog option “Save multiple models in a single file” and use the “Save relative to model mymap.mrc” so that the atom coordinates are save relative to the coordinate system of the density map you fit into.


> On Oct 6, 2016, at 4:26 PM, Martin Lawrence  wrote:
> 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!
> Thanks,
> Martin
> Martin Lawrence
> Department of Chemistry and Biochemistry
> Montana State University
> Bozeman, MT 59717
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