[Chimera-users] classifying contact interactions

[M. Shahid]

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 at 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 at 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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