If your resolution is high enough to support a deviation, then I don't see why not. I would probably stick with a chair conformation unless you are at high resolution or have convincing other evidence for the deviation. What often works well (and is easiest) is to define the 4 atoms that are the "seat" of the chair as a plane in your restraints file. Manually position the outer atoms in the up and down positions of the chair, and then refine. Simple, and pretty effective. Good luck-
Steve ________________________________ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Rex Palmer Sent: Monday, August 16, 2010 12:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Lactose refinement We are attempting REFMAC refinement of a protein structure which is complexed with lactose. One of the rings (the one oriented away from the protein) loses the chair conformation which is flagged as a problem by COOT check chiral volumes. Is there anything we can do to restrain the ring as a chair and would this necessarily be a valid move? ie why can't the conformation deviate from the norm? Rex Palmer Birkbeck College Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
