[Chimera-users] Amino acid scanning

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 30 08:43:33 PDT 2013

Hi Alper,
I don't have an answer for the second question -- there are many possibilities which I haven't used or compared with each other -- but you are right that Chimera does not calculate free energies.

As for the first question, your commands look reasonable to me.  For the clash-report and PDB files you might want to include the whole pathname (including file location).  On my Mac it might be something like this:

write #0 /Users/meng/Desktop/mutations/test_22ile.pdb

Also if you were rotating the view of the structure around but you want to keep the same coordinates as the original structure (except for the mutation, of course) you could use the "relative" keyword, for example:

write relative #0  #0 /Usersmeng/Desktop/mutations/test_22ile.pdb

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 Jul 30, 2013, at 4:35 AM, Alper Yilmaz <alperyilmaz at gmail.com> wrote:

> Hi,
> We are conducting a study to figure out the best amino acid mutation for increased affinity for a particular metal ion. 
> I'm pretty novice in this field so I wanted to get suggestions as to my approach makes sense or not.
> I'll write a demo script (more probably python script) to substitute certain amino acids with all standard amino acids and then minimize the structure. 
> As far as I know, Chimera can not calculate free energy, so I will save the PDB files and then use another program to calculate the free energy.
> My first question is, whether the commands below are appropriate for my purpose or not? The sample below is a snippet from an exhaustive list. I preferred to save the information regarding clashes before the minimization just to keep record.
> swapaa ala :22.a
> findclash :22.a log true saveFile clash_report_22ala
> minimize nogui true
> write #0 test_22ala
> swapaa val :22.a
> findclash :22.a log true saveFile clash_report_22val
> minimize nogui true
> write #0 test_22val
> swapaa ile :22.a
> findclash :22.a log true saveFile clash_report_22ile
> minimize nogui true
> write #0 test_22ile
> ...
> My second question is, when I have many PDB files, which software is suitable for calculating the free energy for each.

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