Re: [ccp4bb]: Riding Hydrogens (fwd)

[Daniel Anderson <dha@mbi.ucla.edu>]

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Finally, a CCP4 topic on which I have something to offer!

When the Richardson's visited us some years ago,
they seemed torn between treating
hydrogen bumps as a validation tool or as a refinement restraint.

I have been using riding hydrogens in shelxl refinements because
it turns on the hydrogen anti-bump restraint.
In the first cycles after adding hydrogens, shelxl's gripe list
includes many, many hydrogen bumps, then the whole model
"relaxes", reducing R, Rfree, and the gripe list.
By "relaxed" I mean for example that the heavier atoms along a side chain
squirm to place the hydrogens into nice staggered (rather than
eclipsed) locations.

Well, that's what I think shelxl does.

Happy Friday,
    Dan Anderson

("squirm" is in the dictionary www.m-w.com with my intended meaning)

---------- Forwarded message ----------
Date: Fri, 6 Sep 2002 16:56:27 -0700
From: Ethan Merritt <merritt@u.washington.edu>
To: Jason Yano <jkyano@scripps.edu>
Cc: ccp4bb@dl.ac.uk
Subject: Re: [ccp4bb]: Riding Hydrogens

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Oh, and for another discussion on the utility of adding hydrogens
to medium-resolution structures you might want to have a look at
the Richardson lab web pages on model validation.

	http://kinemage.biochem.duke.edu/validation/valid.html

The key notion here is not one of R or R-free, but simply that any
correct structural model for the heavy atoms must leave room for
the attached hydrogens. If there is no room, then something must
be wrong, or at least non-optimal. So adding hydrogens can be
used as a structure validation tool.

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002


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