Re: [ccp4bb] How to refine a solution obtained by molecular replacement
Hi Sun, For 2.5A data you can try phenix or arp/warp to autobuild the the model using the phase form MR ,then you can get the most of model you want if you are lucky enough or you need more manual bulding or another cycle MR again . Good luck! liu Sun Tang wrote: Dear All, Recently I solved a structure at 2.5 A with PHASER, with two molecules in assymetric unit. There are no short contacts in the solution. However, the Rfree stays at about 50% after the refinement of rigid boby and restrained refinement in CNS. The sequences homology is about 30%. What is the usual way to deal with this kind of problems? Should I just refine the backbone of the structure and then build the side chains? Your suggestions are greatly appreciated!!! Best wishes, Sun
Re: [ccp4bb] How to refine a solution obtained by molecular replacement
Dear Sun, if I remember correctly phaser already carries out a rigid body refinement of its solution. To avoid and remove as much model bias as possible, I suggest you look at the solution from phaser and build _as_ _much_ _as_ _possible_ BEFORE you do any further refinement, i.e., try to match the sequence, correct side chains, etc. Only once you cannot do any bettermanually you should run a refinement program and after that again build as much as possible, etc. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 17 Mar 2009, Sun Tang wrote: Dear All, Recently I solved a structure at 2.5 A with PHASER, with two molecules in assymetric unit. There are no short contacts in the solution. However, the Rfree stays at about 50% after the refinement of rigid boby and restrained refinement in CNS. The sequences homology is about 30%. What is the usual way to deal with this kind of problems? Should I just refine the backbone of the structure and then build the side chains? Your suggestions are greatly appreciated!!! Best wishes, Sun
Re: [ccp4bb] How to refine a solution obtained by molecular replacement
I've found CNS's simulated annealing composite omit maps to be very useful in situations like this to avoid phase bias. RESOLVE's prime and switch offers similar functionality, but I've had less experience with it. ho UC Berkeley
Re: [ccp4bb] How to refine a solution obtained by molecular replacement
Dear All, Thank you very much for all your suggestions. They are very helpful in my further refinements. I am adding some more information about the problem: 1) The Z-score is 11.2 and LLG is 125. 2) The model has 390 aa while my structure has about 440 aa. Please let me know of any further suggestions. I will try all your suggestions and let you know the updated information about the refinement. Best regards, Sun From: Ho-Leung Ng hole...@berkeley.edu To: CCP4 bulletin board CCP4BB@jiscmail.ac.uk; suntang2...@yahoo.com Sent: Wednesday, March 18, 2009 12:10:29 AM Subject: Re: How to refine a solution obtained by molecular replacement I've found CNS's simulated annealing composite omit maps to be very useful in situations like this to avoid phase bias. RESOLVE's prime and switch offers similar functionality, but I've had less experience with it. ho UC Berkeley
