[Chimera-users] Generating Spheres tutorial

Francesco Pietra chiendarret at yahoo.com
Fri Oct 5 09:09:49 PDT 2007

I am running Chimera 1.2422 on a Linux desktop and DOCK6.1 and DMS on a
scp-linked Linux parallel machine.

Following the "Generating Spheres" tutorial of dock, I verified that DMS works
correctly. Though, I am unable with Chimera to visualize properly the rec.ms
and sphere_cluster.pdb (the files I have generated are identical to those

With rec.ms I am unable to visualize the small molecule inside the protein.
With sphgen_cluster.pdb I can only see disconnected pieces, thogh placed as
expected from the tutorial. Clearly, I need to pass to a Chimera tutorial.
Which one(s) for the case in point?

I apologize for the pedestrian questions. Though, coming from organic chemistry
and ab initio calculations, I am finding Amber9, DOCK6.1, DMS, and Chimera no
minor burden. Quite interesting, however.


francesco pietra

Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. 

More information about the Chimera-users mailing list