From: Elaine Meng <meng@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@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@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 […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@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@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
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@cgl.ucsf.edu> wrote:
*From: *Elaine Meng <meng@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@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@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@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@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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