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Hi U Sam When you say "R increases and Rfree decreases or vice versa" it's important to consider which variables they are increasing/decreasing with respect to. During a given run of Refmac (or whatever) with N iterations, where you optimise a *fixed* set of atomic/group/overall parameters with preset *fixed* weighting parameters, you are trying to achieve convergence (i.e. no further significant changes in any of the parameter values) and to minimise Rwork. Actually to be more accurate, you are aiming to maximise the total LLG (restraints + X-ray data). This will happen automatically unless something is badly wrong (i.e. the optimiser should be optimising if it's working properly!). Note that the 'LLG' column printed at the end of a Refmac run often decreases initially then increases, so I assume it is only the LLG contribution from the X-ray terms. However, if you then change the set of parameters to be refined (e.g. by adding water, ions etc), or you change the weighting parameters, then you are aiming to minimise Rfree *at convergence*, i.e. you repeat the refinement run with the new fixed set of parameters and weights until convergence, then compare the new *final* Rfree with the old *final* Rfree and accept whichever parameter/weighting set gave you the lower value. Again, to be more accurate you should be monitoring the free LLG (i.e. larger value), not Rfree, but unfortunately Refmac doesn't appear to calculate this - other programs e.g. Buster/TNT do (some tests I did showed that Rfree is not optimal at the optimal LLGfree and vice versa). HTH! -- Ian > -----Original Message----- > From: [log in to unmask] > [mailto:[log in to unmask]] On Behalf Of U Sam > Sent: 25 April 2007 20:29 > To: [log in to unmask] > Subject: R and Rfree > > Hi Everybody, > I have small query. > I am feeding ions and correcting few residues into my final structure. > If R increases and Rfree decreases or vice versa in the > subsequent refinement, which one I should accept and go forward. > Thanks. > Sam > _________________________________________________________________ > Discover the new Windows Vista > http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE > > 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 [log in to unmask] 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