Re: [COOT] H-bonding in sphere refine
Hello Kenneth, On 06/05/2022 23:48, Kenneth Satyshur wrote: I use the sphere refine in coot all the time. It's great. And when I turn on 'Environmental Distances'. I can see the H-bonding to the residue. Great. I have recently been using Isolde in ChimeraX to fit 3 A CryoEM density. When I select a residue, turn on H-bonding, it shows all the nearest H-bonding. And when I run the MD to fix up the problems, the H-bonds move in real time with the MD. Thus I can see where the H-bonds of a neighbor may in fact be messing up the phi/psi in question. Sometimes it is a sidechain that decides to pick a fight with the backbone. Pulling on the offending group can resolve the phi/psi. This is especially true of beta sheets with its alternating peptide bonds. My question is, can coot display the H bonds within a 'sphere refine' radius so I can see all the H-bonding, and watch it more in real time. Short answer no. Longer answer... One can add hydrogen bonds to the refinement (set_refine_hydrogen_bonds(1)), but one can't see them during refinement. coot 1 users can visualize the hydrogen bonds using coot.calculate_hydrogen_bonds(imol). I have recently been working on the interactive non-bonded contacts, so it may not be much more work to add interactive hydrogen bond representation also. What I have not yet done (but is on the list) is dynamic updating of non-bonded contacts list (and thus hydrogen bonds) during refinement (this is the sort of thing that has been delayed ~3 years by me having to do the infrastructure/gui/graphics work as a result of the Python 3 upgrade (for what that's worth)). Is there a 'radius' parameter for 'environmental distances'? No, it applies the the residue at the centre of the screen. p.s. coot is so powerful I keep learning new things the more I use it. Thanks Paul. :-) Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] H-bonding in sphere refine
I use the sphere refine in coot all the time. It's great. And when I turn on 'Environmental Distances'. I can see the H-bonding to the residue. Great. I have recently been using Isolde in ChimeraX to fit 3 A CryoEM density. When I select a residue, turn on H-bonding, it shows all the nearest H-bonding. And when I run the MD to fix up the problems, the H-bonds move in real time with the MD. Thus I can see where the H-bonds of a neighbor may in fact be messing up the phi/psi in question. Sometimes it is a sidechain that decides to pick a fight with the backbone. Pulling on the offending group can resolve the phi/psi. This is especially true of beta sheets with its alternating peptide bonds. My question is, can coot display the H bonds within a 'sphere refine' radius so I can see all the H-bonding, and watch it more in real time. Is there a 'radius' parameter for 'environmental distances'? thanks kas p.s. coot is so powerful I keep learning new things the more I use it. Thanks Paul. Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, College of Ag and Life Sciences: Department of Bacteriology; School of Medicine and Public Health: Departments of Biomolecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center (Small Molecule Screening Facility) University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
