Dear Prof. Read, Thank you for your detailed explaination. I think now I am clear about what each set of scores represent. But what do you mean by what the .sol should show? I did "make it up" by selecting two solutions sets from two different runs, and I am sorry for not making it clear at the begining.
Thank you so much! Sincerely, Chen On Wed, Jul 31, 2013 at 6:35 AM, Randy Read <rj...@cam.ac.uk> wrote: > 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 > >
