[Chimera-users] All-by-all distances

Shawn sms1592ss at gmail.com
Tue May 9 06:02:31 PDT 2017


Wow! Thank you so much for the quick response. This is exactly what I was
looking for. It worked!

Best,
Shawn Sternisha

On Mon, May 8, 2017 at 9:26 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

>
> *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>
>
> 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
> […etc…]
>
> 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
> […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 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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