On Mar 31, 2009, at 6:28 AM, ROSETTA FORESTIERO wrote:

Hi I have a receptor and more ligands, I want find h-bond between receptor and each ligand using a scripts shell but i have some problem. Can you help me?

Hi Rosetta, Depending on your situation you may not need a script. Let's say you have the receptor open as model 0 and the ligands in models 1 and higher. You could write all the ligand-receptor H bonds to a file named "hbonds.info" with: sel #1-end; hbonds selRestrict cross saveFile hbonds.info The output should be pretty easy to use to find the H bonds to the individual ligands. If you need individual files for some reason, a script like this would work: open 0 receptor.pdb open 1 ligand.001.pdb hbonds intramodel false saveFile ligand.001.hbonds close 1 open 1 ligand.002.pdb hbonds intramodel false saveFile ligand.002.hbonds close 1 etc. You would probably generate the script using some programming language you are familiar with. Lastly, you can use Python to get Chimera to execute the above commands directly, something like: from chimera import runCommand runCommand("open 0 receptor.pdb") for ligNum in range(1, 1001): runCommand("open 1 ligand.%03d.pdb" % ligNum) runCommand("hbonds intramodel false saveFile ligand.%03d.hbonds" % ligNum) runCommand("close 1") You would put the above in a file ending in ".py" and execute it in Chimera simply by opening the file. --Eric