Hello Randy, I'm chiming in about the last sentence in your reply:
> Finally, I would suspect that getting a significantly lower LLG for two > copies of a dimer means that the dimer in your structure is slightly > different from the dimer in the model. > Will you please be more specific about what you consider "significantly lower" (or higher) for LLG scores? And how does this difference translate to differences among TFZ scores? I have wondered this especially when a Phaser MR result from use of a smaller part (i.e. one domain, 64% of the sequence) of a structure differs by a few units relative to a result from use of a larger part (i.e. two domains, 90% of the sequence) of the protein; the difference in my case was a top TFZ score of 42.5 using the one-domain search model, but a lower TFZ score of 36.9 for the two-domain model. Even more interesting to me is when the TFZ scores vary by quite a bit more between two phaser runs that used two different, but 100% sequence identical, one-domain search models; in this case the top TFZ scores were 18.7 versus 42.5, for the two models that differed only in the coordinate position of ~20 out of 290 residues (a lid for the enzyme). Regards, Emily. Best wishes, > > Randy Read > > ----- > 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 > > > On 18 Sep 2017, at 16:24, Andrew Leslie <and...@mrc-lmb.cam.ac.uk> > wrote: > > > > Regarding the warning message "The top solution from a TF rescoring did > not pack”, I get this on all the PHASER jobs that I have run recently, but > looking through the PHASER log file I cannot see any evidence for packing > failure. > > > > It may be that the failure is buried in an obscure place in the very > long log file, but if I search for “pack” then I get the output summarised > below, all of which, apart from the ADVISORY, suggests to me that there is > no problem at all with the packing. > > > > Perhaps someone on the PHASER team can cast light on this. > > > > Andrew > > > > > > Extracts from PHASER log file: > > > > > > TRANSLATION FUNCTIONS > > --------------------- > > > > Target Function: FAST LETF1 > > Translation Packing Function applied: top peak will pack > > Translation Packing Cutoff: 50% > > Sampling: 1.82 Angstroms > > > > > > =============================================== > > ---------------- > > PACKING FUNCTION > > ---------------- > > > > There are 4 solutions to pack > > Packing analysis > > 0% 100% > > |=====| DONE > > > > <!--SUMMARY_BEGIN--> > > Packing Table > > ------------- > > Solutions accepted if pairwise clashes less than 10 % of trace atoms > > #in #out Clash-% Symm TF-SET ROT TFpk# TF TFZ > SpaceGroup > > 1 Top1 0.741 -- 1 1 1 325.94 26.03 P 1 > > 2 2 1.058 -- 1 2 1 293.29 24.34 P 1 > > 3 3 0.952 -- 1 3 1 245.70 21.88 P 1 > > 4 4 0.847 -- 1 4 1 211.49 20.11 P 1 > > > > 4 accepted of 4 solutions > > 4 pack of 4 accepted solutions > > > > ================================================== > > ------------------- > > TRANSLATION PACKING > > ------------------- > > > > Translation Packing Cutoff: 50% > > All solutions have been packed > > > > ================================================== > > Packing Fast Search Translations... > > 9871 peaks > > 500 peaks over 1049.74 checked for packing > > Translation peak 1 first to be kept > > Done > > > > <!--SUMMARY_BEGIN--> > > New Top Packing Fast Translation Function FSS = 2181.37 (TFZ=46.3) at > Trial #1 > > <!--SUMMARY_END--> > > > > Top Peaks Without Clustering > > Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean) > > There was 1 site over 67.5% of top > > 1 peak selected > > The sites over 67.5% are: > > # Frac X Frac Y Frac Z FSS Z-score > > 1 0.719 0.122 0.890 2181.4 46.35 > > > > Top 1 translations before clustering will be rescored > > Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 1 > > 0% 100% > > |==| DONE > > > > Packing LLG Translations: pass 1 of 11... > > 1 peaks > > No peaks over 1878.46 - no packing check > > Packing LLG Translations: pass 2 of 11... > > 1 peaks > > 1 peaks over 1878.46 checked for packing > > Translation peak 1 first to be kept > > Done > > Exit: found a peak that packs > > > > -================================================== > > > > *** AND THEN *** > > ------------------------------------------------------------ > ------------------------------ > > Advisory: The top solution from a TF rescoring did not pack > > ------------------------------------------------------------ > ------------------------------ > > > > > > -================================================== > > - > > > >> On 18 Sep 2017, at 15:06, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > >> > >> You need to provide a bit more information. > >> > >> First of all about the data processing.. > >> > >> Is the space group correct? > >> ways of being misled are: > >> Non-crystallographic translations with a shift of ~0.5 along an axis - > say a. This will generate absences in the odd h 0 0 reflections and can > make the space group appear to be P 21 21 21 whilst it is really P 2 21 21.. > >> > >> Perfect twinning can have the same effect. In an orthorhombix space > group this can usually only occur if two axes have approximately the same > length, but the data processing stats can indicate if that is the case. > >> > >> Then - re PHASER. The packing rejection criteria may be set too > severely - that seems the case for your solution. > >> > >> Best check on any MR solution is: does it refine - give it 20 cycles of > mindless refinement and see if the R and FreeR go down. > >> > >> Then look at the maps and see if there are obvious corrections to be > made.. > >> > >> Eleanor > >> > >> On 18 September 2017 at 14:59, Satvik Kumar <kumarsatvi...@gmail.com> > wrote: > >> Dear Crystallographers, > >> > >> I am trying to solve a structure in the space group P212121. Based on > Matthews coefficient, there are 4 molecules in the asymmetric unit. > >> > >> Based on my limited reading about using of Phaser, I understand that a > single chain should be used as search model even though many copies are > present in asymmetric unit. Am I correct? > >> > >> So when I use a single chain as search model and ask Phaser to search > for 4 molecules, Phaser identifies a single solution with a warning "The > top solution from a TF rescoring did not pack" and a warning "Search > request requires more scattering than defined in composition. Composition > increased to accommodate search components". But the final values reported > "PAK=2 LLG=1065 TFZ==22.6" indicate that phaser has solved the problem. > >> > >> Can anyone please explain the meaning of the warning. > >> > >> When I inspect the arrangement of the chains (attachment), I observe > minimal contact between the chains and a large cavity in the center. Can a > crystal form this way? > >> > >> I have also tried using the dimer as search model and asking phaser to > search for 2 molecules. Even in this case, Phaser finds a single solution > but the warning and the advisory still appear as before. The numbers > reported reduce a bit to "PAK=1 LLG=722 TFZ==29.2". > >> > >> Please help me in understanding these results. > >> > >> Thanks, > >> Satvik > >> > >> > >> > > > -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott
