[Chimera-users] Fetch by ID EMDB + fit PDBs enhancement suggestion

Tom Goddard goddard at sonic.net
Fri Sep 18 10:55:31 PDT 2015


Hi Ingvar,

  I’ve made Chimera fetch the mmCIF file if the PDB format file is not available.  This will be in tonight’s daily build.  Unfortunately the Chimera mmCIF file reader is very slow since it is written all in Python — opening 3j9z.cif, 150,000 atoms, took 40 seconds.  I also fixed fetch EMDB + fit PDBs to show the map even if one or more PDBs are not found.  Thanks for reporting these bugs.

	Tom


> On Sep 18, 2015, at 5:10 AM, Ingvar Lagerstedt  wrote:
> 
> Dear Chimera,
> 
> Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID.  The map is retrieved but not opened in Chimera.
> 
> The two main reasons that the model is not available:
> A. The model is only available in mmCIF format.  Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries.  They are only distributed as mmCIF (and PDBx) files.  This is common for say ribosomes.  EMD-6315 with fitted model 3j9z is an example.  Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.
> 
> B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval.  In this case it would be nice if the map was loaded.
> 
> Many Thanks,
> Ingvar




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