Hi Tim Sorry I can't help you with Phenix, I would just like to point out that from a theoretical standpoint it's very difficult to say a priori what the value of the ADP variance should be. Since the resolution is 2.4 I assume you're talking about isotropic ADP's. Essentially all of the contribution to the differential isotropic ADP comes from transverse librational motion, i.e. perpendicular to the bond, and it's almost impossible to place a limit on the magnitudes of the libration amplitudes. Measured bond vibration amplitudes parallel to the bond direction are 1 or 2 orders of magnitude lower than those usually observed in proteins (they are even an order of magnitude lower than those observed in small molecules where the average B is around 5 to 10), so the bonds are effectively rigid. The isotropic ADP is of course the mean of the principal components of the anisotropic ADP tensor, so all one can say is that the isotropic ADP difference is the mean of 3 numbers, 1 of which is zero and the other 2 you don't really know!
-- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Tim Gruene > Sent: 30 January 2008 13:42 > To: [email protected] > Subject: ADP variance restriction in phenix > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Good day, > > we are currently refining a 2.4 protein structure using phenix.refine. > > I would like to know how to reduce the adp-variance. We have > jumps from 60 > to 90 and back between adjacent residues and I do not like it. > > I scanned the documentation I found on the web but did not > find what I was > looking for. > > Cheers, Tim > > - -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > > iD8DBQFHoH6eUxlJ7aRr7hoRAnHDAJ41oNg2xbQ8uOcDg8qvf3iwAdN1CQCgyUrk > D1poszqt/Sx78f2MuLzz4h8= > =eQEr > -----END PGP SIGNATURE----- > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
