[Chimera-users] Generating Spheres tutorial

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 5 10:07:17 PDT 2007

Dear Francesco,
Neither of the files contains molecules:

- rec.ms is a dot molecular surface.  It might be hard to see if the 
dots are very small; if you zoom out it will be more obvious.

- sphere_cluster.pdb just contains the sphere centers in PDB format, 
which will look like a bunch of disconnected dots.  In the "wire" 
representation these may also be hard to see, so you might show them as 
"bs" or "sphere" (note that the sphere representation will not show the 
sizes computed by sphgen, it will just make them all bigger balls of 
equal size).

All you need to do is open those files with File... Open.  I just used 
the files downloaded from the DOCK tutorial to test this.  If you want 
to see the receptor or ligand at the same time, you have to 
additionally open those files.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 5, 2007, at 9:09 AM, Francesco Pietra wrote:

> 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
> downloaded).
> 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.
> Thanks
> francesco pietra

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