Hello Bala, (1) I can't tell what happened without seeing the data. It sounds like what you did would work, but perhaps in editing the prot1 file you would also need to renumber the residues (if chain A and chain B both had residue 10, if you don't renumber there will be two residues number 10, which could cause a problem) and remove "TER" lines to make sure it is really interpreted as a single chain. (2) After you open everything you can just use "Actions... Focus" in the menu to make everything visible (or command "focus" or "window"). This will zoom out. It will not put each molecule in the center, because it will still use the coordinates that are in the files. The only way to put the molecules in the center is to focus on the reference structure and then match the others onto it, such as with MatchMaker or "match." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 4, 2009, at 8:08 AM, Bala subramanian wrote:

Hello all,

1) I have to superimpose two protein structures based on sequence matching say prot1 and prot2. Precisely matchmaker. My prot1 is a cryo electron microscopy structure, the structure is not continuous, it has missing residues and hence its pdb contains 3 Chains. My prot2 is a crystal structure, having one chain. I need your suggestion in superimposing these two structure wherever the sequences are matching.

What i tried: I opened pro1 pdb and changed all chain names as A ( it contains chain A,B,C). Then i tried to superimpose with prot2, but matchmaker doesn work.

2) when i open molecules one by one, i need all the molecules appear in the center of the chimera window. How to set this in chimera. After opening the first pdb, when i open the second one, it is invisible.

Thanks, Bala