Hi Shahid, It depends what you want. If those are the results you want (all aromatic-aromatic contacts), it would be the right approach. If not, you would want to use more filtering on the output using names, or deleting some atoms before the calculation as Eric described, to narrow down the results. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 31, 2009, at 2:32 AM, M. Shahid wrote:
Dear Elaine,
Thanks again for the good information. I have done it the way you said and it is really a lot of work, but i was thinking was it the right way or not. When I select aromatic ring, all aromatic-aromatic contacts between both residues and ligand aromatic atoms are displayed.
Best regards,
-- Shahid.
On Thu, Oct 29, 2009 at 6:11 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: 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 .......... .... ... .. .
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