Hello Charlie, Thank you very much for your comments. I mostly agree with you. However, as far as I know most of the complexes structures are solved with MR with the their apo-enzyme as search model and refined the structures with CCP4 or CNS. I tried the simulated annealing omitting the residue and 4 neighboring residues on each side and I found the conformation are essentially the same. I also tried to use composite omit-map calculation in CSN but I gave it because it took several days of computer time but only finished only 1/4 of the calculation. I understand the starting from the beginning is one choice. I wonder whether there are other easier ways in CCP4 to deal with this situation because this problem is quite common in refinement. I appreciate all the replies to my questions and I say "Thank you very much" here. Best, Sun
--- On Sat, 7/26/08, Charles W. Carter Jr. <[EMAIL PROTECTED]> wrote: From: Charles W. Carter Jr. <[EMAIL PROTECTED]> Subject: Re: [ccp4bb] question about getting rid of model bias in refinement To: CCP4BB@JISCMAIL.AC.UK Date: Saturday, July 26, 2008, 3:15 PM Sun, I'm most of the way to one side of this debate: I believe that it is not possible to emerge fully from model bias without avoiding it in the first place with experimental phases. I may be overly pessimistic, but have considerable experience supporting at least skepticism. My interpretation of the experimental result you describe is that the covariances among the parts of the structure you left in place and those side chains you omitted is so strong and extensive that you'll never see the correct density coming back upon refinement, because other parts of the structure are ever so slightly off their true mean positions to compensate for the (evidently false) positions of the residues you omitted. Bill's suggestion that you actually refine the structure using simulated annealing without the omitted residues is an improvement over what you did, but it will require many cycles to get a much better approximation, and there is really no way to be sure when you can be confident. Starting the entire refinement over is a more aggressive strategy. If you decide to try this, you should examine the projection of the residue by residue real-space correlation coefficients across the entire sequence to ensure that you have only one population of values and delete all residues that comprise any population that has a distinctly different real-space correlation coefficient, building them back into the structure as it refines. That is, you should ensure that you don't begin refining any residues at the very beginning for which there is evidence that they might be different from their positions in your molecular replacement model. Charlie On Jul 26, 2008, at 2:12 PM, William G. Scott wrote: Hi Sun: It might be worth doing a simulated annealing omit refinement in phenix or CNS, with the residues in question omitted. CNS also allows you to make a composite-omit map. I haven't seen that in phenix yet but presumably it is doable. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 25, 2008, at 10:53 PM, Sun Tang wrote: Hello Everyone, I have a question about getting rid of model bias in refinement with refmac. I solved the structure with molecular replacement. After final refinement of the structure, I found out some key amino acids in the structure and wanted to make sure their conformations are correct. I omitted these amino acids (by setting occupancy to zero) and refined the structure. I manually fit the amino acids into the density and refined the structure again. I found these amino acids return to the precious conformations even though the conformations I fit were different. Should I omit these amino acids from the beginning of the refinement? What is the best way to get rid of the model bias? Your suggestions are greatly appreciated! Best, Sun **********UNCrystallographers NOTE new website url****************** [EMAIL PROTECTED] http://xtal.med.unc.edu/CARTER/Welcome.html Department of Biochemistry and Biophysics CB 7260 UNC Chapel Hill, Chapel Hill, NC 27599-7260 Tel: 919 966-3263 FAX 919 966-2852
