[Chimera-users] [Chimera] #14773: Connectivity problems with CIF file

Eric Pettersen pett at cgl.ucsf.edu
Thu Jun 30 16:19:12 PDT 2016

Hi Clarisse,
	While it is theoretically possible to add methyl groups as donors in Chimera, it is by no means easy.  Firstly, you’d have to come up with geometric criteria as per the source Chimera uses:

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. <http://www.ncbi.nlm.nih.gov/pubmed/9007693> Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.

Then you would have to modify the FindHBond module to add methyl donors and their geometry criteria.  The learning curve would be steep.
	Since you have explicit hydrogens on your structures, a simpler alternative that may be good enough is to use the Find Clashes/Contacts tool to find “contacts” between methyl hydrogens and hydroxyl oxygens.  Just run the tool, select methyl hydrogens (e.g. “sel methyl & H”), designate them as a set to check, select the hydroxyl oxygens (“sel hydroxyl & O”), designate them as the second set, set checking to be between the two sets, then perhaps check contacts using the default parameters, or whatever parameters you felt were appropriate.
	BTW, you have to get tomorrow’s build to have the “methyl & H” thing work, because there was a bug where “methyl” only selected the methyl carbon.


	Eric Pettersen
	UCSF Computer Graphics Lab

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