Yes, I can see how that message would be confusing! This comes from a new feature. Phaser now does a relatively liberal packing test as part of rescoring the fast translation results with the full likelihood function. Peaks that are rejected at this stage aren’t counted for the top peak height used to define the cutoff for what is stored for the proper packing test and eventual rigid-body refinement. This turns out to be very useful for models that are small fragments, particularly helices in Arcimboldo, where the initial searches tend to put molecules on top of symmetry axes.
The confusing part is that you get the advisory even if the particular translation search where a peak was rejected didn’t even yield a score as high as the one that ended up being chosen. The bit in the log file about increasing the composition suggests that what is in your model has more scattering matter than what you defined for the corresponding part of the structure in the composition definition. If the change wasn’t big, you don’t need to worry, but if there was a big discrepancy it’s worth sorting out where it comes from. 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. 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 >> >> >> >
