[Chimera-users] classifying contact interactions

[Eric Pettersen]

Hi Shahid,
	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):

	del ~aromatic
	sel :LIG

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:

	del ~sel

then find clashes as above.  Then on a new copy of the system find  
contacts between atoms with the charges reversed.
	Like I said:  ugly!

--Eric

                         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.
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