Hi all, Actually, what I think has happened here is that Phaser has limited the resolution to what it estimated was needed to get a clear enough solution, and then the final refinement was carried out with all the data. The signal-to-noise is lower with limited data, but it’s a price that seems worth paying to get the answer more quickly. The final refined LLG of 1848 is a very large number, and the TFZ-equivalent calculation indicates that, if the translation search had been carried out with the final refined orientation using all the data, the TFZ would have been a very respectable 30.2. That’s probably a better number to look at now, with the new adaptive Phaser searches.
Of course, I agree completely that you would also like to see that the correct space group gave a much higher score with the same data than the alternative space groups! Phaser chose a single solution, so it was probably at least reasonably clear. We’re stlll working on how to give the clearest possible indication at the end of a run as to whether you should be confident that it is correct. 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 28 Jan 2015, at 19:33, Matthew Franklin <mfrank...@nysbc.org> wrote: > Hi Jeorge - > > Something seems to have changed for the worse in this MR run. In your > earlier posting, where you failed to find a solution in P222, your log file > had solutions with RFZ=23.4, generally a clear indication of a correct > rotation function solution. (You didn't include this log file as text, so I > can't extract the relevant lines to show you.) But in this run, your log > file shows a solution with RFZ=5.7, which is much more marginal. The space > group choice for the translation function shouldn't affect the results of the > rotation function. What else did you vary - is the search model different? > > In addition to what Roger suggested, other indications that you have the > right solution come from the translation function tables. You should have a > very clear distinction between the correct solution and incorrect solutions, > like this: > >> Fast Translation Function Table: Space Group C 1 2 1 >> ---------------------------------------------------- >> #SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble >> 1 1 4328.56 (29.62) - - - - 3gi8_fab >> 1 2 4294.35 (26.16) - - - - 3gi8_fab >> 1 3 4252.29 (27.13) - - - - 3gi8_fab >> 1 4 3746.99 (13.34) 3725.62 (12.73) - - 3gi8_fab >> 1 5 3467.72 ( 5.02) 3467.43 ( 5.02) 3464.58 ( 4.94) 3gi8_fab >> 1 6 3545.59 ( 6.93) 3482.22 ( 5.27) - - 3gi8_fab > > Trials 1-3 are correct, while trials 5-6 are incorrect. (Trial 4 is probably > also correct, but wasn't tested further by Phaser.) > > You also want to check that the packing test did not throw out one of these > high-scoring translation solutions (e.g. your RFZ=23.4 solution). If that > happened, this could mean you need to trim away some loops in your search > model. > > Good luck, > > Matt > > > > On 1/28/15 12:25 PM, jeorgemarley thomas wrote: >> Hi, all >> >> As per the suggestions, I hv done with the phaser MR and the solution has >> come with screw axes P 21 21 21. here I am attaching the output text from Mr >> and sol file. So Now should I go ahead with this? Please suggest. >> >> Thank you very much in advance ! >> >> On Tue, Jan 27, 2015 at 9:33 PM, jeorgemarley thomas <kirtswab...@gmail.com> >> wrote: >> Thank you so much to all for your kind concern. >> >> >> >> Jeorge >> >> On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs >> <kay.diederi...@uni-konstanz.de> wrote: >> Dear Jeorge, >> >> you'll find some information about this in >> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination >> . A practical and easy way is described in >> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless >> >> HTH, >> >> Kay >> >> On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene <t...@shelx.uni-ac.gwdg.de> >> wrote: >> >> >Dear Jeorge, >> > >> >XDS make no claim to determine the SPACE GROUP but rather the LAUE >> >GROUP, as only the latter is taken into account during data integration. >> > >> >This is definitely so during the indexing step (IDXREF.LP), but even in >> >CORRECT, when systematic absences are sometimes indicated, XDS does not >> >really choose the space group. >> > >> >Best, >> >Tim >> > >> >On 01/26/2015 05:46 AM, jeorgemarley thomas wrote: >> >> Hello Dr. Randy >> >> Here is the IDXREF.LP I got in which, on the basis of quality of fit, I >> >> went for this space group well I would also try for the other screw axes. >> >> So should I Integrate the data from beginning with all possible screw axes >> >> of orthogonal space group? I am attaching the IDXREF.LP screen shot here. >> >> >> >> Jeorge >> >> >> >> On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett <rrowl...@colgate.edu> >> >> wrote: >> >> >> >>> Did you search all 8 possibilities of screw axes, e.g. P2221, P21212, >> >>> P212121, etc? >> >>> >> >>> Roger Rowlett >> >>> On Jan 25, 2015 4:50 AM, "jeorgemarley thomas" <kirtswab...@gmail.com> >> >>> wrote: >> >>> >> >>>> Hi, I have processed the data using XDS and space group found to be P 2 >> >>>> 2 >> >>>> 2 (16) and I used the phaser MR for first phase determination. The >> >>>> model I >> >>>> have used has has more than 70 % sequence identity, when I run the >> >>>> phaser I >> >>>> got the message which I have attached here. And only sum. file I got as >> >>>> an >> >>>> output. Does any one have suggestion what should I do ? I would highly >> >>>> appreciate your kind suggestions. Thank you in advance. >> >>>> >> >>>> >> >>>> >> >> >> > >> >-- >> >Dr Tim Gruene >> >Institut fuer anorganische Chemie >> >Tammannstr. 4 >> >D-37077 Goettingen >> > >> >GPG Key ID = A46BEE1A >> > >> > >> >> > > > -- > Matthew Franklin, Ph. D. > Senior Scientist > New York Structural Biology Center > 89 Convent Avenue, New York, NY 10027 > (212) 939-0660 ext. 9374 >
