Friends, I want to choose certains atoms and get the x,y,z coordinates of the center. Kindly write me how to do it in chimera. Bala
Hi Bala, I have been using the free program Mercury to calculate centroids. It allows you to pick any number of atoms, least-squares fit them to a plane, and calculate a centroid. I usually do this and then output the xyz coordinates and past them into a pdb file with a dummy atom name or you can assign the atoms to boron or something else not in your structure. You can then open your pdb files and use chimera to superimpose centroid atoms of multiple structures or make measurements and pictures. Mercury also allows you to least squares fit planes to atoms or points and measure angles between intersecting planes. These would be great analysis tools to add to Chimera! If you need any help or more info don't hesitate to email me. Cheers, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen@caltech.edu ********************************************** On Apr 2, 2009, at 1:06 AM, Bala subramanian wrote:
Friends,
I want to choose certains atoms and get the x,y,z coordinates of the center. Kindly write me how to do it in chimera.
Bala _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Bala, David had good suggestions, but if you just want the center with equal weights for each atom then you can use Chimera's 'cofr' command to get that if you're careful. For instance: cofr :10.a & aromatic ring will report the center of the aromatic ring in residue 10 of chain A to the status line and to the Reply Log. However, it reports it in lab coordinates, not model coordinates, so you have to be careful not to move your model after opening it -- so that the model and lab coordinates are the same. If you do move it, you should be able to use the "reset" command to get the coordinate systems back in sync. This presumes that you don't have other models open. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 1:06 AM, Bala subramanian wrote:
Friends,
I want to choose certains atoms and get the x,y,z coordinates of the center. Kindly write me how to do it in chimera.
Bala _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Bala subramanian -
David Chenoweth -
Eric Pettersen