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?

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 1 ligand.001.pdb

hbonds intramodel false saveFile ligand.001.hbonds

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