Hi Shahid,
For (d) there is not really any trick, it is just using the residue and atom names. For example, if you knew C1-C6 in LIG are an aromatic ring, for aromatic-aromatic contacts to PHE you could look for lines in the contacts output with PHE CG,CD1,CD2,CE1,CE2,CZ such as:
LIG 1 C1 PHE 168.A CD2 -0.163 3.488
As I mentioned this would be a lot of work since you would have to know all the atom/res names for a particular type of functional group such as aromatic ring. Also, I don't think this would work for your system because looking at what you sent below, your LIG atoms are not named uniquely (all the carbons are just named C, all the nitrogens named N, etc.).
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Oct 29, 2009, at 4:10 AM, M. Shahid wrote:
Dear Elaine,
Dear Eric,
Thanks a lot for suggestion of using an alternate way of classifying the contact interactions.
I am currently using it with step by step selection of different types. And its working great!!! thanks again.
Could you please also give me some hints on the other way you mentioned in (d) below in conversation?
Best regards,
--
Shahid.
On Mon, Oct 26, 2009 at 9:02 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
(d) yet another approach is to just get all the contacts of all types and filter them afterwards. However, that would require you to figure out the types of interactions based on the residue and atom names, which might be a lot of work. If using this approach, you might want to remove all the hydrogens first, since they would generally provide a large amount of redundant information.
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
.......... .... ... .. .