[Chimera-users] Ramachandran plot statistics

[Nadia Raboana]

Hi,

It works perfectly, thank you for helping me. 

Best regards,

Nadia



Sent from Windows Mail


From: Elaine Meng
Sent: ‎February‎ ‎8‎, ‎2015 ‎12‎:‎52‎ ‎AM
To: Nadia Raboana
CC: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Ramachandran plot statistics



Hi Nadia,
You would have to decide for yourself what probability cutoff you want to use as the boundary between allowed and disallowed.

First assign the probabilities to the residues:  in the Ramachandran Plot dialog, click the button at the bottom to “Assign Residue Probabilities” (or use the ramachandran command option “assign”):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ramachandran.html>

Then in Select by Attribute (Chimera menu: Select… By Attribute Value) choose attributes of “residues” with Attribute: ramaProb … that will show a histogram of the probability values.  Then you can move the green bars to enclose the range of probabilities you want to select.  After you use that dialog to select everything above your cutoff probability, then you can get a count of the selected residues by clicking the green magnifying glass at the bottom right corner of the Chimera window to show the Selection Inspector.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

Then you would divide by the total number of amino acid residues to get the percentage.  You could count the total number of amino acid residues, for example, by using command “select protein” and then clicking the green magnifying glass.

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

On Feb 7, 2015, at 4:49 AM, Nadia Raboana <nadia_raboana at hotmail.fr> wrote:

> Hello,
> I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions.
> Thank you for answering me.
> Best regards,
> Nadia Raboanatahiry
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