AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: David A. Case (
Date: Thu Jan 24 2008 - 20:18:48 CST

On Thu, Jan 24, 2008, Seth Lilavivat wrote:
> In the NMR refinement tutorial, it suggests setting ialtd=1 if your
> structure is distorted due to an opposition of restraints and force field.
> Is it ok to refine the structure using the ialtd=1 or is this meant as a way
> to help find bad restraints?

You can do refinements with ialtd=1, but you would want to look carefully at
any large NOE violations that are encountered, and figure out if you can live
with them or not. Sometimes a "soft" restraint like this will end up throwing
out important information.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | skype: dacase La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to