Question: Calculate Radius of Gyration [python 3]
gravatar for ac.research
16 months ago by
ac.research10 wrote:

Hello Everyone,

I am trying to find a way to calculate the Rg (Radius of Gyration) of a protein.

I searched through Biopython but I could not find a way to do it.

Is it possible to do this calculation from Biopython? Is there a script someone has written that I can use, even if it uses a library different then Biopython?

Thank you for your help.

ADD COMMENTlink modified 16 months ago • written 16 months ago by ac.research10

Hi, maybe you can try PyMOL library. There is a python example to do this calculation: Radius_of_gyration

ADD REPLYlink written 16 months ago by Sparrow_kop190

Hmmm, the script from pymol does not work out of the box, but I modified it and it works now. Thanks.

But the issue is that I cannot call it from within another python script (in other words I cannot run the script with python3 rather pymol -c which means I cannot include it in other non-pymol python scripts.

So it is a temporary fix for now, but I would still rather use a better function, something from biopython or if possible a raw mathematical function (I understand how Rg works, but I am having difficulty implementing the math in python).

ADD REPLYlink written 16 months ago by ac.research10

I fixed the PyMol script to make it a stand alone script capable of running on python3 independent of PyMol. Here is a link to it in case someone wants to use it in the future :-)

ADD REPLYlink written 16 months ago by ac.research10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1171 users visited in the last hour