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Is this a Phaser bug or am I misinterpreting ?
by Phil Jeffrey 05 Dec '12

05 Dec '12

Phaser from CCP4 6.3.0 built via fink running on OSX 10.6.8 in 64-bit mode. This is a snippet from a much larger run, ongoing. In multiple instances the order of the LLG and the Z-score in the translation function are not in sync: (42.16, 40.23, 40.18 vs 5.14, 5.24, 4.82) and looks like the Z-scores are still shown in the peak rank order before rescoring, while the LLGs are after rescoring. SET #5 of 6 TRIAL #60 of 115 ---------------------------- Search Euler = 263.0 82.1 85.7, Ensemble = ensemb3 ANNOTATION: RFZ=3.6 TFZ=3.8 PAK=0 LLG=26 LLG=30 Known MR solutions SOLU SPAC C 1 2 1 SOLU 6DIM ENSE ensemb3 EULER 30.6 65.7 246.9 FRAC 0.90 0.00 0.17 BFAC -5.14 Grid sampling: 0.825029 Angstroms Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean) Top 360 translations before clustering will be rescored Calculating Likelihood for TF SET #5 of 6 TRIAL #60 of 115 0% 100% |=========================================================================| DONE Scoring 1 randomly sampled translations Generating Statistics for TF SET #5 of 6 TRIAL #60 of 115 0% 100% |==| DONE Top Peaks With Clustering ------------------------- # Rank of the peak after rescoring search points (#) Rank of the peak before rescoring search points LLG Log-Likelihood Gain Z-Score Number of standard deviations of LLG above the mean FSS Fast Search Score Select all peaks There were 159 peaks # (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top 1 6 0.842 0.923 0.779 +42.16 5.14 0 2 52.58/ 52.58 2 3 0.369 0.865 0.553 +40.23 5.24 37 2 53.18/ 53.18 3 10 0.743 0.937 0.261 +40.18 4.82 48 2 50.69/ 50.69 #SITES = 159: OUTPUT TRUNCATED TO 3 SITES

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Re: [phenixbb] log files for refinement (was: completeness using Intensities vs. structure factor)
by Pavel Afonine 05 Dec '12

05 Dec '12

Hi Yarrow, thanks for sending log files. Completeness reported in log files reflects the content of input MTZ data files: *32.log:* (...) F-obs: (...) Miller array info: (...)/reflectionsFreeR_1.38A.mtz:F_New(+),SIGF_New(+),F_New(-),SIGF_New(-),systematic_absences_eliminated Observation type: xray.amplitude Type of data: double, size=325598 Type of sigmas: double, size=325598 Number of Miller indices: 325598 Anomalous flag: True Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.901282 Completeness with d_max=infinity: 0.901259 (...) and *35.log:* (...) I-obs: (...) Miller array info: (...)/reflectionsFandIFreeR_1.38A.mtz:IMEAN_New,SIGIMEAN_New,systematic_absences_eliminated Observation type: xray.intensity Type of data: double, size=181940 Type of sigmas: double, size=181940 Number of Miller indices: 181940 Anomalous flag: False Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.992202 Completeness with d_max=infinity: 0.992164 (...) The numbers above are reported before anything else is done, that is they reflect exactly what's in input MTZ files. Somehow you managed to loose ~10% of data when converting Iobs into Fobs. How did you do this conversion? In theory this is possible since French&Wilson Iobs->Fobs conversion may result on some number of reflections lost. Note, when phenix.refine does IMEAN->Fobs conversion (35.log file) this does not result in ~10% loss. So based on looking at log files I can say it's not phenix.refine that manipulated your data or reported it wrong. You lost reflections at previous steps. Pavel On 12/4/12 4:57 PM, Yarrow Madrona wrote: > Hi, > > Here are the log files for refinement you asked for. > > 35.log is refined with Intensities. The MTZ file has a slightly different > name but it is the same MTZ. One had Intensities taken out of it because I > didn't think I needed them any longer. > > 32.log is refined with structure factors. Intensities were removed. > > Thanks for your help! > > -Yarrow > > >

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completeness using Intensities vs. structure factor
by Yarrow Madrona 05 Dec '12

05 Dec '12

Hi, (Phenix v.1.8.1-1168) I recently refined a structure using experimental Intensities and compared it to the same structure refined with calculated structure factors. I know if you provide intensities Phenix.refine will convert to structure factors. I am not sure if it runs truncate or what. Anyway, I get this in the log file which matches my completeness in the scala log file: Completeness in resolution range: 0.992202 Completeness with d_max=infinity: 0.992164 When I run using structure factors (Truncate run in Scala) I get the following: Completeness in resolution range: 0.901282 Completeness with d_max=infinity: 0.901259 Perhaps Scala did not merge anomolous and non-anomolous data? This does not may a whole lot of sense to me. Is some data thrown out? Can someone explain? Thank you. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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parameters for averaged kick maps
by Jose M de Pereda 04 Dec '12

04 Dec '12

Dear all, I would like to compare averaged kick maps obtained using different “kick sizes”. Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps? In phenix.refine, the “ordered_solvent” section has keywords to control the generation of kick maps: kick_map { kick_size = 0.5 number_of_kicks = 100 } But, it seems to me that these can not be used during the generation of maps or maps’ coefficients. Related with this issue, does phenix.refine always use the same kick size or does it adjust it ad hoc (e.g. based on ML error estimates)? Thanks a lot, Jose -- ------------------------------------------------------------ Jose M de Pereda, PhD Instituto de Biologia Molecular y Celular del Cancer (IBMCC) Spanish National Research Council - University of Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294817 Fax: +34-923-294795 http://xtal.cicancer.org/ ------------------------------------------------------------

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table 1
by So Jay 04 Dec '12

04 Dec '12

Hi, I was using generate table 1 utility in phenix-1.8.1-1168. The data was processed with HKL2000 and model was refined using Autobuster. In the table I find two entries for Multiplicity and R-sym were blank.I was wondering if there is any particular reason for this. ThanksJay

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Similar 2Fo-Fc maps, very different e/A^3 levels (absolute levels)
by Sam Stampfer 04 Dec '12

04 Dec '12

Dear Phenix group, I am trying to decide which electron density map to use for rebuilding my structure in Coot. Both 2Fo-Fc maps appear quite similar at the 1 sigma level but the absolute electrons per cubic Angstrom (e/A^3) is very different. When contoured at 1.00 rmsd in coot, these are the e/A^3 levels (Coot calls them absolute levels): Map #1 2Fo-Fc: 0.0044 e/A^3 Map #2 2Fo-Fc: 0.0832 e/A^3 Map #1 was generated using a twinning operator that is typically required for this crystal form. Map #2 was generated without the twinning operator and it tends to have slightly better 2Fo-Fc density, and there is a bit more density (or noise?) in the Fo-Fc map. The structure was refined in Phenix and gave a similar Rfree regardless of whether a twinning operator was used. What does it mean to have this 20-fold difference in electrons per cubic Angstroms for my maps? Which map should I use? Thanks for your help! -Sam PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3 level.

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pseudotranslation and twinning problem
by Rajeshwer Sankhala 03 Dec '12

03 Dec '12

I am new to crystallography. I have collected data for 26 kDa protein with a maximum resolution of 2.25A in I 41 space group. I have a poor model for molecular replacement (~15-20% identical). When i did xtriage run, it suggested -h,k,-l twinning law and indicated about pseudo-translation. Now when i am running Phaser for molecular replacement i am getting very low LLG (less than 100) and TFZ score (5-6). Can anyone suggest which parameters or setting i should use to improve my LLG score and get a best model for refinement. Thanks Raj

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dev-1227: problem reading in tls parameters from refmac or tlsmd
by Boaz Shaanan 02 Dec '12

02 Dec '12

Hi, In the TLS pulldown I tried to upload tls parameters from either refmac (.tls) or tlsmd (.tlsin) through the 'load' button, according to the suggestion in this section, but it complains about wrong format of the file. Am I doing something wrong? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Specify particular columns from data files on the command line
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all (again)- I'm trying to run DEN refinement in Phenix from the command line. How do I specify certain columns from multiple data files (in my case, 2 MTZ files) to be used? For example, the Rfree flags from one and the hkl data from the other. Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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DEN refinement
by Morten Groftehauge 30 Nov '12

30 Nov '12

Hi guys, Two quick questions about DEN refinement: 1) If gamma refines to 0 does that mean that I should run DEN refinement again with the output model? Or should I do a refinement and then another DEN? Since gamma = 0 the refinement should be allowed a possibility of moving the structure further towards the reference restraints in my mind. 2) If gamma refines to 1 it means that my reference model is inappropriate, right? Not really much of a question, I know. And I know that DEN refinement is in beta but it would be nice if you outputted the optimal gamma and weight for the refinement to the GUI. Actually it would be nice if the did that for geometry weights and xray weights too when one optimizes them. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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