[Chimera-users] To retrieve intermediate results while using Minimize Structure

Conrad Huang conrad at cgl.ucsf.edu
Mon Nov 1 15:40:50 PDT 2010

To expand on Elaine's answer, there are no intermediate PDB files 
generated in Chimera's minimization process.  Chimera uses the MMTK 
toolkit to perform minimization and MMTK maintains its own in-memory 
universe of atomic coordinates.  Every few steps, Chimera updates its 
molecules from MMTK atomic coordinates.  At no point is any file 
generated.  So the only way to get "intermediate" files is to use 
Elaine's suggestion of running a few steps, saving the PDB file and 


On 11/1/10 9:09 AM, saumyak at ebi.ac.uk wrote:
> Hello,
> I am using Chimera's Minimize structure for protein minimization. I was
> hoping if you could suggest me a way to retrieve intermediate PDB files
> that are generated during the minimization procedure.
> Many thanks,
> Saumya
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