Dear Chen, For each component that is placed, Phaser reports the Z-scores for the rotation function (RFZ) and translation function (TFZ), along with the number of packing clashes (PAK) at this point and the LLG. For the top solution at that point in the search, Phaser also reports the TFZ-equivalent (TFZ=) score, which is what the Z-score would have been for the translation search if the refined orientation from the rigid-body refinement had been used. We introduced the TFZ-equivalent to eliminate the dependence of the TFZ on the quality of the orientation used for the particular translation search that (after refinement) ended up giving the best solution. However, it takes some CPU time to compute a random sampling of translations for that orientation, so we only do it for one solution after adding each component.
Your .sol file doesn't quite make sense in terms of what it should show. Did you make it up to illustrate your point? What you might see is that, for the top solution, the first LLG value (from placing the first component) is lower the the corresponding LLG value for a solution lower in the final list. However, you might see a TFZ== entry immediately after the first LLG for whichever solution had the highest LLG at that point in the search. If a solution that was worse after placing the first component ends up with the top LLG after adding the second component to that solution, then there will be a TFZ== entry after the second LLG value (corresponding to the LLG after placing the second component. I hope that helps! There's also an explanation on our Phaser Wiki: http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Annotation, which gets into some even more obscure aspects of this annotation line. Randy Read On 31 Jul 2013, at 01:24, Chen Zhao <chenzhaoh...@gmail.com> wrote: > Dear all, > > I am sorry for my new-comer question, but I am not clear what the multiple > RFZ, TFZ, PAK and LLG scores belong to after each solution set in the phaser > output (eg. .sol) file. My bet is that each of them corresponds to each of > the solutions listed below, but I am not sure. Also I know that TFZ== > represents the TFZ score based on the refined orientation, but why does it > sometimes appear in the middle instead of at the end? > > One example could look like this: > > SOLU SET RFZ=5.4 TFZ=3.6 PAK=0 LLG=67 TFZ==1.8 RFZ=2.2 TFZ=5.1 PAK=3 LLG=91 > LLG=102 > SOLU SPAC XXX > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU ENSE ensemble1 VRMS X > SOLU ENSE ensemble2 VRMS X > > SOLU SET RFZ=4.2 TFZ=2.8 PAK=0 LLG=51 RFZ=3.1 TFZ=5.1 PAK=1 LLG=71 LLG=86 > TFZ==5.3 > SOLU SPAC XXX > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU 6DIM ENSE ensemble1 EULER X X X FRAC X X X BFAC X > SOLU ENSE ensemble1 VRMS X > SOLU ENSE ensemble2 VRMS X > > Thank you so much! > > Sincerely, > Chen ------ 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
