[Chimera-users] classifying contact interactions
meng at cgl.ucsf.edu
Sat Oct 31 10:09:09 PDT 2009
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 C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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,
> On Thu, Oct 29, 2009 at 6:11 PM, Elaine Meng <meng at cgl.ucsf.edu>
> 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
> 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.).
> 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,
> On Mon, Oct 26, 2009 at 9:02 PM, Elaine Meng <meng at cgl.ucsf.edu>
> (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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