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):

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:

then find clashes as above. Then on a new copy of the system find contacts between atoms with the charges reversed.

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.