[Chimera-users] finding contacts among protein atoms

[Elaine Meng]

Hi Nicky,
Upon further examination of my testing results, at this shorter cutoff distance (less negative overlap) you should also set the H-bonding allowance to zero so as not to miss any pairs within 4 angstroms.  So whether you use the single-command shotgun approach or a separate command for each residue, include “hb 0”, e.g.

findclash #0:1 test #0&protein overlap -0.3 hb 0 log true

At this shorter cutoff, a large proportion of the contact pairs will be H-bonding. The H-bond allowance is normally used to avoid identifying H-bonding pairs as a “clash” because they can come closer together as a favorable interaction than they can to other atoms with which they are not H-bonding.  However, you are using the command to identify contacts in general, not only unfavorable clashes.  The default criteria (in the FInd Clashes/Contacts GUI) for identifying contacts are overlap -0.4 and hb allowance 0.
Best,
Elaine

> On May 3, 2017, at 1:35 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Nicky,
> You could specify all protein atoms instead of just the CA atoms.  #0 means model 0, @ca means  atoms named CA, so "#0 at ca” means CA atoms in model 0...  “protein” means all protein atoms, or to limit it to only model 0 (if you had multiple models open) “#0&protein”.  E.g.
> 
> findclash #0&protein test self overlap -0.3 log true
> 
> (which by default excludes atom pairs 4 or fewer bonds apart, or in the same residue, but these can be adjusted with command options)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> 
> I think I’d determined empirically when formulating my previous reply that overlap -2.3 gives the pairs within 6 angstroms, so I changed it in the example above to overlap -0.3 (VDW surfaces up to 0.3 angstroms apart) to give pairs within 4 angstroms.  You could doublecheck using overlap -0.35 or -.4 to see if that gives you any more contacts within 4 angstroms if you want.  Again, the last column in the output is the distance between atom centers.
> 
> However, you’d have to parse the extremely copious output to find which residues' atoms are in contact with which.  
> 
> Another possibility is to use a separate command for each residue to get a separate list, but then making the command script is tedious.  E.g.
> 
> findclash #0:1 test #0&protein overlap -2.3 log true
> findclash #0:2 test #0&protein overlap -2.3 log true
> [etc.]
> 
> A third possibility (beyond my skill set) is to use python to loop through the residues and generate essentially those commands. This page has some tips on python scripting of Chimera commands if you want to try that.
> <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
> 
> I hope this helps,
> 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 May 3, 2017, at 11:43 AM, Nicole Persky <persky at broadinstitute.org> wrote:
>> 
>> Hi Again!
>> So sorry to bother you again, do you by any chance know if there is a command line similar to 
>> 
>> findclash #0 at ca test self overlap -2.3 log true
>> 
>> but instead of finding Ca-Ca distances that are less than 6 angstrom to 
>> use all of the atoms in a residue and look for other atoms/residues that come within 4 angstroms?
>> 
>> Thanks so much!!
>> Sincerely,
>> Nicky
>> 
> 
> 
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