In all versions of Phaser up to the currently distributed ones, the assumed RMS error of the model is used to generate an a priori SigmaA curve for the likelihood target. At the end of the structure solution, the map coefficients are computed by using those a priori SigmaA values to calculate m and D.
So it should indeed be better to go into SIGMAA, Refmac or phenix.refine and generate a map, because the SigmaA values will be refined to reflect the actual agreement between Fo and Fc, not the agreement that was guessed beforehand. Nonetheless, I'm surprised that the difference in quality can be so noticeable. That implies that the initial guess of model quality was far off the actual value, so it would be good to know what Phaser was told about model completeness and either expected RMS error or sequence identity, in cases where the maps were bad. We (by which I mean Airlie) are currently working on putting a SigmaA refinement into the end of the Phaser MR run, so future versions of Phaser won't have this issue. It would be useful if we could get an example or two of where the current version gives really bad maps, so we can verify that the new procedure fixes the problem. Regards, Randy Read On 5 Feb 2010, at 00:48, hari jayaram wrote: > Hi , > I just switched to ccp4-6.1.3 and ran the phaser which is bundled > with the ccp4-6.1.3 release. After molecular replacement I get a > pretty good solution (TFZ 59.2) and output pdb and mtz files. > I am then looking at the maps from the phaser output mtz i.e the FWT , > PHWT map and the FWT PHIC map . Both maps look very crappy and look > like noise. I tried the fft inside of coot and separately as a FFT > inside ccp4 and these maps look bad. So the FWT PHWT calc seem to be > off. > > However , if I take the phaser solution output model and do the sigmaa > myself. The map looks normal and sensible. > > It seems like phaser inside of ccp4-6.1.3 is not generating the output > mtz correctly . > Anyone else seeing this or is there something wrong with my setup. > > > Hari ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
