Hi Boaz, There are two main issues that might complicate your analysis: (1) extra chains or copies of the protein and cofactor within the same PDB file (2) differences in how the cofactor residue is named and its atoms are named For issue (1), you could decide which protein chain(s) you want to work with and delete the others to simplify the situation. Some PDB files are cooperative and give the cofactor molecules chain IDs that match the corresponding protein (residue HEM in chain A is bound to protein chain A, B in B, etc.), in which case it is pretty easy to select whole chains and delete them. Other PDB files are less conveniently arranged, with cofactor molecules given no chain ID or different chain IDs than the proteins that bind them, so even after you delete extra protein chains, there are a bunch of extra cofactor molecules floating around. At this point, I usually select atoms in each of those from the graphics window with Ctrl-Shift-click, hit up arrow to promote the selection to the entire residues, and then delete the selection. The reason you would want to delete extra copies is that if you use the name of the cofactor for matching, that will specify all existing copies, resulting in unequal numbers of atoms to be matched in the two structures. Issue (2) can be even more taxing. IF the cofactor residue has the same name and its atoms have the same names and are in the same orders in all pairs of structures to be compared, you could then use EnsembleMatch. You'd specify the cofactor residue as the atoms to match, e.g. :fad (residues named FAD). Another approach in this situation would be to use the match command, e.g. command> match #1:fad #0:fad (match FAD in model 1 to FAD in model 0). This would reorient the entire contents of model 1 to best fit the specified atoms. The drawback is that sometimes the residues and/or their atoms are named differently or the atoms are in different orders. Rather than peering at the files, you might want to try EnsembleMatch or the match command and see whether the resulting fit and RMSD value are as expected. If not, then the atom naming issue is probably to blame. When the atoms are named differently, you can still use the match command, but you would either have to name all the atoms in corresponding orders, or pick them in the same orders (first in one model and then the other) from the graphics window with Ctrl-Shift- click; both of these approaches are described in the man page for "match": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html This page also describes the iteration option, which could be helpful if the cofactor is in different conformations in the different structures. I hope this helps, Elaine On Mar 7, 2006, at 2:58 AM, Boaz Shaanan wrote:

Hi Chimera prople,

If I want to superimpose proteins on their co-factors (or part of them), is ensembleMatch the way to go or are there other ways to do this ? I'd appreciate your advice.

Regards,

Boaz

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************************************************************* Boaz Shaanan, Ph.D. Associate Prof. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

Phone: 972-8-647-2220 e-mail:bshaanan@bgu.ac.il Fax: 972-8-647-2992 or 972-8-646-1710 *************************************************************

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----- 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