[Chimera-users] Radius of Gyration questions

George Tzotzos gtzotzos at me.com
Thu Apr 6 12:35:53 PDT 2017

Taking a reference PDBID 3n7h, I’ve generated for an MD simulation topology and restart files.

I’ve loaded on Chimera 3n7h and then the starting frame of the MD simulation. 
Used the MatchMaker and found perfect superposition of the protein backbone and two ligands (3n7h is #0 and the ligands #0:129.A and #0.132.B

I run the radius of gyration script (see attached). I found that the radii of gyration for the ligands in the two models are completely different.

#0 center of mass: 12.6543 10.4356 15.4086, radius of gyration: 21.182
#1 center of mass: 42.7381 42.5171 42.6163, radius of gyration: 37.390

I don’t follow why this is so. Any explanation would be most welcome.

A second question regards the units of the radii of gyration. Are they Angstrom or nm?

Thank you in advance


-------------- next part --------------
A non-text attachment was scrubbed...
Name: rad_gyration.py
Type: text/x-python-script
Size: 421 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170406/22b5edf5/attachment.bin>

More information about the Chimera-users mailing list