Hello, I'm new to Chimera and just discovered the FindHBond tool. This tool seems very useful, but unfortunately it draws hbonds between the heavy atoms even when I have hydrogens added. Is there a way to configure this behavior? I'd like the hydrogen bonds to be drawn between the hydrogen and the acceptor atom. It looks rather strange now, especially for the hbonds with relaxed constraints that deviate significantly from the angle made by the hydrogen. See the attached tiff for an example. Also, I'm curious what cutoffs are used. I looked at http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond... but I was hoping for more details. I.e what numbers from the paper are used for the proton-acceptor distances, donor-proton-acceptor angle and the corresponding dihedral angle. Thanks! Greg Friedland Postdoc Joint BioEnergy Instute Sandia National Lab Formerly of Tanja Kortemme's lab at UCSF
Hi Greg, There are many different distance and angle criteria depending on the different donor and acceptor atom types. These cutoffs are in tables 5-8 of the reference cited in the page you were viewing: Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. <http://www.ncbi.nlm.nih.gov/pubmed/9007693> <http://www.springerlink.com/content/m34t237u46784242/> 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 Dec 14, 2009, at 4:32 PM, Greg Friedland wrote:
Also, I'm curious what cutoffs are used. I looked at http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond... but I was hoping for more details. I.e what numbers from the paper are used for the proton-acceptor distances, donor-proton-acceptor angle and the corresponding dihedral angle.
On Dec 14, 2009, at 4:32 PM, Greg Friedland wrote:
I'm new to Chimera and just discovered the FindHBond tool. This tool seems very useful, but unfortunately it draws hbonds between the heavy atoms even when I have hydrogens added. Is there a way to configure this behavior? I'd like the hydrogen bonds to be drawn between the hydrogen and the acceptor atom. It looks rather strange now, especially for the hbonds with relaxed constraints that deviate significantly from the angle made by the hydrogen. See the attached tiff for an example.
Hi Greg, There is no capability for that now. I expect that capability in the 1.5 release, and will add your name to the Trac ticket for that enhancement, so you will automatically get notified when it gets implemented. In the interim, if you execute the attached Python script the hbond donor terminus will be moved to the appropriate proton. Execute the script simple by opening it with File...Open or with the "open" command. --Eric
participants (3)
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Elaine Meng -
Eric Pettersen -
Greg Friedland