<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 31, 2009, at 6:28 AM, ROSETTA FORESTIERO wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi<br>I have a receptor and more ligands, I want find h-bond between receptor<br>and each ligand using a scripts shell but i have some problem.<br>Can you help me?</div></blockquote><br></div><div>Hi Rosetta,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>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:<br></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>sel #1-end; hbonds selRestrict cross saveFile hbonds.info</div><div><br></div><div>The output should be pretty easy to use to find the H bonds to the individual ligands.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If you need individual files for some reason, a script like this would work:<br></div><div><br></div><div>open 0 receptor.pdb</div><div>open 1 ligand.001.pdb</div><div>hbonds intramodel false saveFile ligand.001.hbonds</div><div>close 1</div><div>open 1 ligand.002.pdb</div><div><div>hbonds intramodel false saveFile ligand.002.hbonds</div><div>close 1</div><div><i>etc</i>.</div><div><br></div><div>You would probably generate the script using some programming language you are familiar with.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Lastly, you can use Python to get Chimera to execute the above commands directly, something like:<br></div><div><br></div><div>from chimera import runCommand</div><div>runCommand("open 0 receptor.pdb")</div><div>for ligNum in range(1, 1001):</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>runCommand("open 1 ligand.%03d.pdb" % ligNum)</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>runCommand("hbonds intramodel false saveFile ligand.%03d.hbonds" % ligNum)<br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>runCommand("close 1")<br></div><div><br></div><div>You would put the above in a file ending in ".py" and execute it in Chimera simply by opening the file.</div><div><br></div><div>--Eric</div><div><br></div></div><br></body></html>