[Chimera-users] All-by-all distances

Elaine Meng meng at cgl.ucsf.edu
Mon May 8 18:26:06 PDT 2017

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: Chimera Question
> Date: May 8, 2017 at 6:03:55 PM PDT
> Hi Shawn,
> I’m out sick… please send Chimera questions to chimera-users at cgl.ucsf.edu list.

On second thought, I think I can answer quickly.  However, for future reference please use the user list for Chimera questions and include a informative “subject” line to make it easier for others to find … thanks!

Command:  findclash :lys at n test self overlap -99999 log true

… will put all the Lys N -> Lys N distances (within about 1000 A … just use a larger-magnitude negative overlap  if you think there are longer distances)  in the Log.  It won’t be a table, though, just a list of distances that you would have to process yourself.  Or instead of “log true” (or in addition to it) you could use the “saveFile” option to specify putting the same output into a text file.

Command and options described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>>

Output is like the following example for PDB 2gbp, with distances in the last column:

464 contacts
atom1  atom2  overlap  distance
LYS 191.A N  LYS 189.A N  -1.010  4.290
LYS 223.A N  LYS 227.A N  -1.505  4.785
LYS 246.A N  LYS 300.A N  -3.378  6.658

However I suspect maybe you meant NZ (the end of the sidechain) instead of the backbone N, in which case the command would be something like

findclash :lys at nz test self overlap -99999 log true

… with output like:

465 contacts
atom1  atom2  overlap  distance
LYS 270.A NZ  LYS 276.A NZ  -1.932  5.212
LYS 308.A NZ  LYS 246.A NZ  -2.262  5.542

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 8, 2017, at 4:14 PM, Shawn Sternisha <ssternisha at chem.fsu.edu> wrote:
>> Hello Dr. Meng,
>> Sorry to bother you but I have a question about Chimera that I have not been able to find an answer to, despite intensive web searches. I have seen your name on a lot of useful posts and answers so I figured I would give emailing you a shot. I have been searching for a method to measure all possible distance between Lys residues in a protein in a high-throughput manner. 
>> For example, if my protein has 17 Lys residues, is it possible to generate a table that has distance measurements between the N atoms of all of them. I believe that would be 231 possible distances. Any advice you could provide would be greatly appreciated. Thank you for your time in advance.
>> Best,
>> Shawn Sternisha
>> PhD Candidate, Miller Laboratory
>> Dept. of Chemistry and Biochemistry
>> Florida State University

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