On Sep 5, 2007, at 3:30 PM, Dhiraj Srivastava wrote: I am new to Chimera and i have hard time finding commands like how to select some chain and exclude 1 or 2 residue in that chain?

Hi Dhiraj, There is an "atom specification" syntax that allows you to say exactly which chains, residue numbers, atoms you want. In brief, # means model, : means residue, @ means atom name. There are many examples throughout the documentation, so I'll give one example in this mail and some links to more information: disp :25-30.a,30.b,10 - display residues 25-30 in chain A, residue 30 in chain B, and residue 10 in all chains Here is the "atom specification" man page, includes some examples: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html (besides just using chain, residue, atom name, you can do all kinds of fancy things such as in helix only, near a ligand, etc.) This PDF help sheet has a bunch of examples on its second page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf

also i have a protein with 2 chain. how can i make different model for different chain or different portion of same chain so i can perform some action like clipping on these model independentaly? can any one please help me for these problems?

You can open the same structure more than once, and then delete different parts from the different models. For example, if the structure has chain A and B, open it twice to put it in models 0 and 1, then use these commands: command: delete #0:.b command: delete #1:.a Then model 0 will just have chain A, model 1 will just have chain B. You could instead undisplay (~display) instead of using delete, but I think deleting is easier - later you can't get confused and accidentally display those other parts. Another way is to use a text editor and make new PDB files with just the parts you want before opening them in Chimera, but that is probably less convenient. 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