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 repeating. Conrad On 11/1/10 9:09 AM, saumyak@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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