<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Shahid,<div><span class="Apple-tab-span" style="white-space:pre"> </span>It certainly would be easier if Chimera allowed you to find contacts/H-bonds between two arbitrary sets of atoms rather than between one set and "everything else". I will open a feature-request ticket in our Trac database for this with you on the recipient list so you will know when it gets implemented. It will probably be several months before I have time to get to it.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>In the interim there is an uglier method for getting what you want -- at least for contacts. Basically you delete away all the atoms you don't care about. So to find the aromatic contacts between ligand and non-ligand do this (Favorites->Command Line):</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>del ~aromatic</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>sel :LIG</div><div><br></div><div>then find contacts between selected atoms and all other atoms. You would have to open a new copy of your system (and close the mutilated one!) to find other interactions.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>To get charge interactions first add charges to your atoms with the Add Charge tool. You can then select ligand atoms with more than a certain negative charge and non-ligand with more than a certain positive charge (say .1 for this example) with:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>sel :LIG & @/charge<-0.1 | ~:LIG & @/charge>0.1</div><div><br></div><div>then delete all other atoms with:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>del ~sel</div><div><br></div><div>then find clashes as above. Then on a new copy of the system find contacts between atoms with the charges reversed.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Like I said: ugly!</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Oct 24, 2009, at 8:00 AM, M. Shahid wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear All,<br><br>I have a question regarding the contact interactions between a protein-ligand complex.<br><br>I can retrieve the contacts by the findclash command in --nogui mode as below:<br>chimera --nogui protligcomplex.pdb <a href="http://clash.com">clash.com</a><br> <br>and similarly I can find the hbonds.<br><br>The output I am getting is as below:<br>--------------------------------------------------------------------------------<br>32 contacts<br>atom1 atom2 overlap distance<br> LIG 1 H ALA 265.A O 1.045 1.435<br>LIG 1 O ALA 265.A O 0.550 2.430<br>LIG 1 N GLU 169.A OE2 0.439 2.666<br>LIG 1 H GLU 169.A CD 0.116 2.584<br>LIG 1 O ASN 253.A 1HD2 0.094 2.386<br>LIG 1 H ALA 265.A C 0.090 2.610<br> LIG 1 C ALA 265.A O 0.059 3.121<br>LIG 1 N ASN 253.A OD1 -0.037 3.142<br>LIG 1 C ALA 265.A O -0.039 3.219<br>LIG 1 N GLU 169.A HG3 -0.072 2.697<br>LIG 1 C PHE 168.A HB2 -0.081 2.781<br>LIG 1 N GLU 169.A CG -0.113 3.438<br> LIG 1 N GLU 169.A CD -0.125 3.450<br>LIG 1 N GLU 169.A CD -0.128 3.453<br>LIG 1 C MET 270.A HG2 -0.140 2.840<br>LIG 1 N PHE 168.A CD2 -0.163 3.488<br>.......... .... ... .. .<br>--------------------------------------------------------------------------------<br> <br>Now I want to further classify these contact interactions into more other types:<br>Aromatic and Ionic (anion < - > cation).<br>Is there any way in Chimera to achieve this?<br>Or if I want to do it with some scripting, which atoms I would say are involved in ionic<br> and aromatic interactions considering the distance value as well?<br>I would be very much grateful if someone suggest me a way to do this.<br><br>Thanks,<br><br>Best regards,<br><br>--<br>Shahid.</blockquote></div></div></body></html>