Hi Jonathan, It does not matter if the atoms are in ATOM or HETATM records in the PDB file. For example: (using commands) open 4hhb col byatom show :hem z<5 findclash :hem overlap 0.2 The HEM residues are all in HETATM records. I doublechecked just now and it also works in the Find Clashes/Contacts GUI. There must be something else going on with your file. You could send it to me if you want... Otherwise (1) are you sure there are contacts within your specified parameters? (2) is your PDB format correct? Best, 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 Feb 4, 2008, at 1:06 PM, Jonathan Magasin wrote:

Hello,

I'm trying to use the clashes/contacts tool to explore valid phi/psi angles for L- and D-Ala (as part of a homework assignment; developing a Ramachandran plot for each). The tool worked great for L-Ala but does not report any contacts for D-Ala. (For each, I've snipped just the relevant sections out of a larger PDB. I'm using default params for collision detection, with detection calculated for any movement.)

The difference in the PDB's for L-Ala and D-Ala is that the latter are in HETATM records. I did include the CONNECT info (to explicitly tell Chimera how HETATMs bond) but that did not help.

Perhaps there's something else I must include, or some modification I can make to the HETATMS (element labeling?) so that collision detection will work as with peptides? Or is this a known limitation? (Is there a list of known limitations? I'm a new user.) I'm not

Note that the distance tool works for D-Ala. If I can get collision detection to work, it take much less time.

Thanks in advance.

-Jonathan