[Chimera-users] chimera minimize script

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 9 09:19:39 PDT 2016

Hi Tatsiana,
As the error message suggests, your write command is incorrect and needs a model-number argument, e.g.

write #0 newfile.pdb

There are other options that might also be useful:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 8, 2016, at 7:22 PM, Bylund, Tatsiana (NIH/NIAID) [F] <tatsiana.bylund at nih.gov> wrote:
> Thank you, Eric!
> Do you know how do I save minimized file in a pdb format?
> I tried 
> rc("minimize spec ':1-97.C z<10.0 & :.G|:1-97.C z<10.0 & :.F|:1-97.C' nsteps 100 cgsteps 0")
> rc("write 'newfile.pdb'")
> It does the minimization, but doesn't write the file
> MidasError: "'newfile.pdb'" is not a model number
> Error while processing chimera_mini.py:"
> Thank you!

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