how to find non-bonded interactions between a protein and a ligand?
Hi,
I need to find non-bonded interactions between a protein and a ligand through command line.
Could anyone please suggest which chimera command to use with the syntax?
With regards,
Sam
Hi Sam, There is a “findclash” command for finding favorable contacts and close contacts. It has the same features as in the “Find Clashes/Contacts” graphical interface, so there are many possibilities of different command-line options and the exact command will depend on the settings you want to use: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html
I recommend looking at that page to see the full syntax and the command-line options. You could also first try using the graphical interface (menu: Tools… Structure Analysis… Find Clashes/Contacts) to decide what settings you want to use. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
However, here is one example command using some standard settings for finding contacts, assuming that “protein” and “ligand” specify the desired parts of your structure:
findclash protein test ligand overlap -0.4 hbond 0.0 reveal true
… or if your protein was model #0 and your ligand was model #1:17 and you also want to select the contacting atoms:
findclash #0 test #1:17 overlap -0.4 hbond 0.0 reveal true select true
There are many ways to specify atoms (e.g. protein and ligand) in the command line: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
There is another example of using the “findclash” command in the Opened Interface image tutorial: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html
… and the “Find Clashes/Contacts” too is used in the Structure Analysis & Comparison tutorial: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.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 Jan 21, 2015, at 2:09 AM, Sam Paul D. reachsampaul@gmail.com wrote:
Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam
Hi Elaine, First of all thanks for all the suggestions. I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand. Thanks! Sam
Sent from my iPhone
On 22-Jan-2015, at 02:12, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Sam, There is a “findclash” command for finding favorable contacts and close contacts. It has the same features as in the “F ind Clashes/Contacts” graphical interface, so there are many possibilities of different command-line options and the exact command will depend on the settings you want to use: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html
I recommend looking at that page to see the full syntax and the command-line options. You could also first try using the graphical interface (menu: Tools… Structure Analysis… Find Clashes/Contacts) to decide what settings you want to use. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
However, here is one example command using some standard settings for finding contacts, assuming that “protein” and “ligand” specify the desired parts of your structure:
findclash protein test ligand overlap -0.4 hbond 0.0 reveal true
… or if your protein was model #0 and your ligand was model #1:17 and you also want to select the contacting atoms:
findclash #0 test #1:17 overlap -0.4 hbond 0.0 reveal true select true
There are many ways to specify atoms (e.g. protein and ligand) in the command line: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
There is another example of using the “findclash” command in the Opened Interface image tutorial: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tut orials/squalene.html
… and the “Find Clashes/Contacts” too is used in the Structure Analysis & Comparison tutorial: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.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 Jan 21, 2015, at 2:09 AM, Sam Paul D. reachsampaul@gmail.com wrote:
Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam
Hi Sam, Well, those are the default settings for contacts, so we believe them to be reasonable. However, "optimal" would be too strong a word, and it surely depends on the resolution of the structure, local B-factors, whether you used docking to generate the complex, etc. As stated in the docs, http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html
"For detecting contacts, negative cutoff values of 0.0-(–1.0) Å are recommended along with a hydrogen bond allowance of 0.0 Å. The default contact criteria in the Find Clashes/Contacts graphical interface are –0.4 and 0.0 Å, respectively."
It is a typical example of setting parameters in computational chemistry. Software developers try to suggest something reasonable, but it is often the responsibility of the scientist to always pay attention to and critically evaluate the results, and perhaps explore a range of values to see what happens (especially for quick calculations like this). Often there is NOT one true correct value, and that's one reason they are user-adjustable in the interface.
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 Jan 21, 2015, at 5:50 PM, Sam Paul D reachsampaul@gmail.com wrote:
Hi Elaine, First of all thanks for all the suggestions. I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand. Thanks! Sam
Hi Elaine, Thank you so much for all the helpful suggestions. Regards, Sam
Sent from my iPhone
On 22-Jan-2015, at 23:46, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Sam, Well, those are the default settings for contacts, so we believe them to be reasonable. However, "optimal" would be too strong a word, and it surely depends on the resolution of the structure, local B-factors, whether you used docking to generate the complex, etc. As stated in the docs, http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html
"For detecting contacts, negative cutoff values of 0.0-(–1.0) Å are recommended along with a hydrogen bond allowance of 0.0 Å. The default contact criteria in the Find Clashes/Contacts graphical interface are –0.4 and 0.0 Å, respectively."
It is a typical example of setting parameters in computational chemistry. Software developers try to suggest something reasonable, but it is often the responsibility of the scientist to always pay attention to and critically evaluate the results, and perhaps explore a range of values to see what happens (especially for quick calculations like this). Often there is NOT one true correct value, and that's one reason they are user-adjustable in the interface.
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 Jan 21, 2015, at 5:50 PM, Sam Paul D reachsampaul@gmail.com wrote:
Hi Elaine, First of all thanks for all the suggestions. I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand. Thanks! Sam
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