Hi Kristof AFAIK there's no attractive H-bond term in Refmac, only a repulsive one, and even that is probably between the N/O atoms not between the H atoms themselves, which only 'ride' on their parent atoms (again this is to my knowledge). This is all related to the fact that H atoms don't scatter X-rays very well! So it all depends on the bases refining to their true positions which obviously depends on resolution, data quality, thermal motion and disorder etc.
HTH (though probably not very helpful!) -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of Kristof Van Hecke > Sent: 05 August 2009 10:53 > To: bulletin_ccp4 > Subject: Restraint hydrogen bond Refmac > > Dear, > > When (trying) to refine a DNA-structure (resolution 2.5) using > Refmac_5.5.0072 (CCP4 6.1.1), some of the H-bonds between Watson-Crick > bases are becoming too large. > > Reducing the Matrix weighting term to tighten the geometry, doesn't effect > these H-bond distances much. > Reducing the "VDW SIGMA HBOND" also doesn't solve the problem. > > Adding "external distance restraints" does the trick, but some B-factors > (not the ones involved in H-bonding!) blow up completely. > > Hence, what's actually the best way of tighten H-bond restraints in > Refmac, or am I overlooking some other issues here..? > > > Thank you very much. > > Regards > > Kristof Van Hecke > > > -------------------------------------- > Kristof Van Hecke, PhD > Biomoleculaire Architectuur > Celestijnenlaan 200 F > B-3001 Heverlee (Leuven) > Tel: +32(0)16327477 > -------------------------------------- > > 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 i.tic...@astex-therapeutics.com 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
