Hi Hongnan The standard criterion for choosing the optimum weight(s) is to choose the value(s) that minimise Rfree at convergence of the refinement, i.e. at the local or global maximum of the likelihood function. Axel Brunger and his group have published a lot of nice work in this area. Alternatively maximising the free likelihood (or equivalently minimising the free negative log likelihood) at convergence seems to have a somewhat better statistical justification (see Bricogne, G., Methods Enzymol. 1997, 276, 361-423).
So it's not possible to say whether particular value of the weights are appropriate for your problem, you have adjust them for each individual case. Personally I always use the 'weight auto x' option in Refmac for the X-ray weighting since then the weighting term x seems to stay within a reasonable range (typically between 1 and 4), and is also incidentally the same term used in CNS & (I believe) phenix-refine. I note you are quoting Rfree only to the nearest 0.01 whereas smaller variations than this are probably significant. If you round Rfree like this you won't see the small differences. The big problem with Rfree is that there's no way of knowing what differences are significant, whereas there do exist significance tests for the free likelihood. Hope this helps! Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of conancao > Sent: 01 April 2009 06:13 > To: ccp4 mailing list > Subject: Choosing weighing term > > Dear All: > > Hi. I have a question about selecting weighing term during > restrained refinement using Refmac5 of CCP4 packages. > > For a 300kDa homodimer protein structure at 2.5A, 91% complete. I > obtain optimal R and Rfree by using NCS tight restraints of the peptides > of the two monomers. Weighing term 0.15 gives (R=0.22, Rfree=0.28) and > weighing term 0.1 gives(R=0.23, Rfree=0.28). Higher weighing term gives > larger difference between R and Rfree. > > Is there a criteria or special range of choosing weighing term? Is > weighing term 0.1 too small? I read the references by Ian Tickle (Acta > Cryst D, 1998 and 2000)on R and Rfree ratio, those helped a lot but I > still do not know the key of weighing term. > > Thanks so much. > > Best, > Hongnan Cao > Biochemistry Department > UC Riverside > > > ________________________________ > > 把MSN装进手机，更多聊天乐趣等你挖掘！ 立刻下载！ <http://mobile.msn.com.cn/> 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
