Hi Shahid, 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. 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): del ~aromatic sel :LIG 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. 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: sel :LIG & @/charge<-0.1 | ~:LIG & @/charge>0.1 then delete all other atoms with: del ~sel then find clashes as above. Then on a new copy of the system find contacts between atoms with the charges reversed. Like I said: ugly! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 24, 2009, at 8:00 AM, M. Shahid wrote:
Dear All,
I have a question regarding the contact interactions between a protein-ligand complex.
I can retrieve the contacts by the findclash command in --nogui mode as below: chimera --nogui protligcomplex.pdb clash.com
and similarly I can find the hbonds.
The output I am getting is as below: -------------------------------------------------------------------------------- 32 contacts atom1 atom2 overlap distance LIG 1 H ALA 265.A O 1.045 1.435 LIG 1 O ALA 265.A O 0.550 2.430 LIG 1 N GLU 169.A OE2 0.439 2.666 LIG 1 H GLU 169.A CD 0.116 2.584 LIG 1 O ASN 253.A 1HD2 0.094 2.386 LIG 1 H ALA 265.A C 0.090 2.610 LIG 1 C ALA 265.A O 0.059 3.121 LIG 1 N ASN 253.A OD1 -0.037 3.142 LIG 1 C ALA 265.A O -0.039 3.219 LIG 1 N GLU 169.A HG3 -0.072 2.697 LIG 1 C PHE 168.A HB2 -0.081 2.781 LIG 1 N GLU 169.A CG -0.113 3.438 LIG 1 N GLU 169.A CD -0.125 3.450 LIG 1 N GLU 169.A CD -0.128 3.453 LIG 1 C MET 270.A HG2 -0.140 2.840 LIG 1 N PHE 168.A CD2 -0.163 3.488 .......... .... ... .. . --------------------------------------------------------------------------------
Now I want to further classify these contact interactions into more other types: Aromatic and Ionic (anion < - > cation). Is there any way in Chimera to achieve this? Or if I want to do it with some scripting, which atoms I would say are involved in ionic and aromatic interactions considering the distance value as well? I would be very much grateful if someone suggest me a way to do this.
Thanks,
Best regards,
-- Shahid.