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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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