- phenixbb - phenix-online.org

Re: [phenixbb] pseudo-merohedral twinning or pseudo-symmetry?
by Gino Cingolani 16 Oct '09

16 Oct '09

Laurie, I had a similar problem. Scaling statistics in P212121 were OK, and - of course - no twinning was detected ... but nothing made sense during refinement. Looking at the data more carefully I found that if one rescales in P21, the b-angle was stably refined to 90.20 with ~30% better Rsym than in orthorhombic. When running xtriage on the P21 data, I found the data were indeed "pseudomerohedrally-twinned" with twinning fraction ~0.38. Good luck! Gino

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pseudo-merohedral twinning or pseudo-symmetry?
by Laurie Betts 16 Oct '09

16 Oct '09

Hi - We have a data set that seems to process well in primitive orthorhombic. a=80, b=87, c=114. The data has overall Rsymm around 10% to 2.6 Angstrom, where I/sigI > 2, and Chi-squared is around 1.4. Phenix.xtriage shows some pathology in intensity statistics such that the L-test indicates <|L|> = 0.414 and <L^2> = 0.241, with the L-test Z score = 7.334. The Wilson ratio for acentric refls is 1.774. According the xtriage, There were no "pseudomerohedral" twin laws found, and the comments at the end say "As there are no twin laws possible given the crystal symmetry, there could be a number of reasons......" Is it more likely that this is a case of pseudo-symmetry, or would one not expect the intensity statistics to have the values they do in that case. Also, is the absence of twin laws defined by the fact that proper merohedral twinning is not possible for P222 space groups? Still confused, Laurie Betts

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autobuild
by Colin Levy 16 Oct '09

16 Oct '09

Hi, can autobuild be setup to use kicked maps when starting from a molecular replacement model? Thanks Colin

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Re: [phenixbb] grouped occupancy definitions
by Dr. Mark Mayer 15 Oct '09

15 Oct '09

Hi Pavel, I'm digging in docs and list serv but could not find out, and figured you probably know faster. I need to make an occ.params file for some groups of non adjacent side chains which interact with each other, and associated waters. 1) How do I select ACs 2) How do I constrain water occupancies so that their Q + that of coupled protein atomes does not exceed 1. If I match the AC flags for the waters and side chains will this take care of it. e.g. if residues 2 and 21 have coupled ACs and waters 101 and 102 move in when residue 21 is in one of its ACs how would I define below? refinement { refine { occupancies { constrained_group { selection = chain A and resseq 2 selection = chain A and resseq 21 selection = chain W and resseq 101 selection = chain W and resseq 102 } } Thanks !!! -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mark Mayer Ph.D.

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low resolution refinement question
by Peter Grey 15 Oct '09

15 Oct '09

Dear Phenix users, I refine a large complex with three monomers in ASU at very low resolution - 4.5A - and would like to ask two questions. - Could you give some tips about refinement at this resolution other than rigid body refinement - Can TLS and grouped B-factors work at this poor resolution ? - I would really prefer that rigid body refinement will strictly obey the NCS that was found in the molecular replacement solution. I understand constrained NCS does not exist yet in phenix but is there something approximate that can be used in rigid body refinement ? I tried the conventional restrained NCS and the result was just like without restrains. Thank you for your time , Peter.

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Why is CIF monomer data split into individual files?
by Joe Krahn 14 Oct '09

14 Oct '09

Is there a good reason not to merger all monomer data into a single file, similar to PDB's components.cif? My first thought is that it is a performance issue. However, I wrote a simple CIF parser in Tcl, and found that carefully designed regexp processing can index data segments very fast. The entire components.cif takes just a few seconds. (The key is to use a regexp that matches an entire data block, and not tokenize the whole file.) So, I am thinking that a single merged file might be better. With separate files, there is already a need for a list of residues (mon_lib_list.cif) which could just as well be file offsets. So, even if parsing is not so fast, it is not an issue because we already have an index file. One problem with separate files is that it relies on the 3-letter residue name to be unique. With a merged file, a different database key can be used without concern for filename restrictions. The PDB format was originally designed so that HET 3-letter codes only need a file scope, where HETNAM defines the full name of each HET residue in a file. Everyone has been using HET codes the same as standard residues, which has cause the 3-letter codes to become meaningless database keys rather than useful abbreviations. Eventually, we will run out of 3-letter codes, and will have to change. Why not start sooner rather than later? Even now, there are potential conflicts. For example, CCP4 has DNA residues using a lower-case d, which may not provide a unique filename for non-POSIX case-insensitive operating systems. If anyone actually wants a Tcl CIF parser, I can share it. I only wrote it as a simple and efficient way to read CIF files from a CCP4i script. Joe Krahn

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Re: [phenixbb] Autobuild for very elongated models
by Gino Cingolani 14 Oct '09

14 Oct '09

Thanks Tom! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ---- Original message ---- >Date: Wed, 14 Oct 2009 08:28:09 -0600 >From: Tom Terwilliger <terwilliger(a)lanl.gov> >Subject: Re: [phenixbb] Autobuild for very elongated models >To: Gino.Cingolani(a)jefferson.edu,PHENIX user mailing list <phenixbb(a)phenix-online.org> > >Hi Gino, > >Here is how to specify a mask in phenix.autobuild (see https://www.phenix-online.org/documentation/faqs.htm >#anch68): > >----------------- >How can I specify a mask for density modification in AutoSol/AutoBuild? >If you want to specify a mask, add this command: > >resolve_command_list=" 'model ../../coords.pdb' 'use_model_mask' " >where there are " and ' quotes and coords.pdb is the model to use for >a mask. Note the "../../" because coords.pdb is in your working >directory but when resolve runs the run directory is 2 directories >lower, so relative to that directory your coords.pdb is at "../../ >coords.pdb". You will know it is working if your resolve_xx.log says: >"Using model mask calculated from coordinates" >----------------- >I am not so sure this is the problem, however. I would suggest that >you do a quick composite omit map before refinement on your mr model: >phenix.autobuild data=data.mtz model=MR.1.pdb >composite_omit_type=simple_omit >It is important that this start with you MR unrefined model so that >you have no worries about model bias. This procedure will omit a >region, refine, calculate a 2Fo-Fc map for the omitted region, then >repeat for all other parts of your model and paste them all together >and put it in >AutoBuild_run_1_/OMIT/resolve_composite_map.mtz >which you can use to calculate a map with LABIN="FP=FP PHIB=PHIM >FOM=FOMM" (you need to include the FOM). >If this map shows density for your whole model...you are in great >shape and the problem may indeed be the mask. If it does not...then >the model may not be very close and it may be difficult to proceed. >All the best, >Tom T > >On Oct 14, 2009, at 7:57 AM, Gino Cingolani wrote: > >> Hi Everyone, >> >> I am trying to solve a very elongated structure (~180A-long) formed >> by two long a-helices. I have a good MR solution (Log-Likelihood >> Gain ~168.537 to 3.0A resolution), which refines OK immediately >> after MR (Rfactor/Rfree 46/50%). The electron density has clear side >> chain features and high res data is available to ~2.1A resolution. >> >> Logically, I should be able to plug everything into Autobuild and >> get a good final model (or at least something better than my input >> MR solution). I have tried a million time using different parameters >> and datasets, but Autobuild always breaks up my long helical model >> into short helical bundles, that refine to random Rfree. In other >> words, if my starting MR model is a continuous >> 80aa-long helix, Autobuild fragments it into three helices of ~30aa >> each packed laterally (I see back my initial model if I visualize >> symmetry-related atoms in Coot). >> >> In parallel, I have made the following observation. >> If I use DM to improve my phases, prior to Autobuild, I noticed that >> something similar happens. DM gives great density for less than half >> of my long helix while the rest is flattened. >> If I look at the solvent mask generated by DM, it basically flattens >> half of my elongated model. It seems that at least DM fails to >> generate a solvent mask that makes sense with such an elongated >> structure (by the way, the unit cell is a=25, b=37, c=220 in >> P212121). This problem can be circumvented in DM where >> an outside solvent mask can be inputted, but what about in phenix? >> >> Is it possible that Autobuild is failing because Resolve also makes >> a poor solvent mask? Is there a way to see and/or edit the solvent >> mask generated by Resolve? Or even better, can I input a new solvent >> mask in Autobuild? >> >> Thanks in advance for the feedback! >> >> Gino >> >> >> ****************************************************************************** >> Gino Cingolani, Ph.D. >> Associate Professor >> Thomas Jefferson University >> Dept. of Biochemistry & Molecular Biology >> 233 South 10th Street - Room 826 >> Philadelphia PA 19107 >> Office (215) 503 4573 >> Lab (215) 503 4595 >> Fax (215) 923 2117 >> E-mail: gino.cingolani(a)jefferson.edu >> ****************************************************************************** >> "Nati non foste per viver come bruti, ma per seguir virtute e >> conoscenza" >> ("You were not born to live like brutes, but to follow virtue and >> knowledge") >> Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > >Thomas C. Terwilliger >Mail Stop M888 >Los Alamos National Laboratory >Los Alamos, NM 87545 > >Tel: 505-667-0072 email: terwilliger(a)LANL.gov >Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >PHENIX web site: http:www.phenix-online.org >ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB >CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss > > > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb

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Autobuild for very elongated models
by Gino Cingolani 14 Oct '09

14 Oct '09

Hi Everyone, I am trying to solve a very elongated structure (~180A-long) formed by two long a-helices. I have a good MR solution (Log-Likelihood Gain ~168.537 to 3.0A resolution), which refines OK immediately after MR (Rfactor/Rfree 46/50%). The electron density has clear side chain features and high res data is available to ~2.1A resolution. Logically, I should be able to plug everything into Autobuild and get a good final model (or at least something better than my input MR solution). I have tried a million time using different parameters and datasets, but Autobuild always breaks up my long helical model into short helical bundles, that refine to random Rfree. In other words, if my starting MR model is a continuous 80aa-long helix, Autobuild fragments it into three helices of ~30aa each packed laterally (I see back my initial model if I visualize symmetry-related atoms in Coot). In parallel, I have made the following observation. If I use DM to improve my phases, prior to Autobuild, I noticed that something similar happens. DM gives great density for less than half of my long helix while the rest is flattened. If I look at the solvent mask generated by DM, it basically flattens half of my elongated model. It seems that at least DM fails to generate a solvent mask that makes sense with such an elongated structure (by the way, the unit cell is a=25, b=37, c=220 in P212121). This problem can be circumvented in DM where an outside solvent mask can be inputted, but what about in phenix? Is it possible that Autobuild is failing because Resolve also makes a poor solvent mask? Is there a way to see and/or edit the solvent mask generated by Resolve? Or even better, can I input a new solvent mask in Autobuild? Thanks in advance for the feedback! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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use get_cc_mtz_pdb to calculate the cc between model and map
by 丁玮 13 Oct '09

13 Oct '09

Hi, everyone: When I use get_cc_mtz_pdb to calculate the cc between model and map, two values is output: （1）Overall map correlation: （2）Map correlation in region of model: What is the different between them? Whether the "Map correlation in region of model" is the correlation between model and the density map superimposing on it and the "Overall map correlation" is the correlation between model and the overall density map? Thanks a lot! dream dingding830106(a)sina.com 2009-10-14

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autosol import failed
by Jan Abendroth 13 Oct '09

13 Oct '09

Hi all, I am trying to run Phenix AutoSol on a SAD data set. Sadly enough, it fails on me during reading in the mtz file with the error message below. The same happens with both intensities or amplitudes. phenix version 1.5-2 run through the gui where I read in the mtz file and specified I+, I-, ... Any ideas? Thanks Jan ~~~~~~~~~~~~~ error message: ImportRawData_output_files ImportRawData Run 3 Tue Oct 13 18:14:37 2009 NOTE: Input labels currently restricted to: I(+),SIGI(+),I(-),SIGI(-) Note also: a group of labels needs to be enclosed with quotes Skipping labels I(+) SIGI(+) I(-) SIGI(-) which do not match requested labels **************************************** AutoSol Input failed -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

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New GUI, MTZ, multiple data sets
by Graeme Winter 12 Oct '09

12 Oct '09

Hi Folks, I just tried reading an MTZ file full of MAD data (from xia2) with the new GUI, and it seems like you can't read more than one data set from a given file - is this the case? It did correctly find all of the columns that were in there. Reading in scalepack format files, one per wavelength, seemed to work fine. Browse then selecting the same file again didn't seem to work, couldn't find the "add another dataset" button... it of course works just fine from the command-line with the .eff file. Thanks, Graeme

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Re: [phenixbb] Does PHENIX exclude Rfree reflections in maps?
by Thomas C. Terwilliger 12 Oct '09

12 Oct '09

Hi Pavel and Joe, I carried out a test to see if (1) excluding a super-free set completely from automated structure solution affects the results and (2) if the super-free R that results is different from the standard free R obtained with all data and excluding the free set only from refinement. Here are the results: A = structure B, C and D are for the run with a super-free set excluded from all calculations. B and C are work and free R for the reflections included in the calculation. D is the R for the super-free set. E and F are work and free R for the same datasets, run in the same way, but without any super-free set. A B C D E F ---super-free-run---- --standard run-- structure work free super-free work free 1029B 0.31 0.38 0.41 0.29 0.36 1038B 0.22 0.26 0.26 0.24 0.28 1071B 0.28 0.33 0.35 0.26 0.30 rab3a-sad 0.31 0.35 0.38 0.29 0.34 rnase-p 0.28 0.32 0.31 0.28 0.29 calmodulin 0.26 0.27 0.27 0.27 0.29 cobd-sad 0.24 0.26 0.26 0.24 0.28 insulin 0.27 0.30 0.29 0.25 0.26 nsf-n 0.23 0.26 0.26 0.21 0.24 ut-synthase 0.24 0.29 0.28 0.24 0.28 mean 0.26 0.30 0.31 0.26 0.29 Conclusions: (1) super-free is very nearly the same as free in the matched set. (2) leaving out super-free data does not make a lot of difference in these actual cases. (Perhaps it might in worse data sets) (3) so it would be ok to take out super-free set, but it is not necessary. All the best, Tom T >> Hi Pavel and Joe, >> >> I'm glad you put that option in, Pavel. However for model-building it is >> not so straightforward. Normally we are building into density-modified >> maps. Density modification works poorly when a significant set of >> reflections is excluded, so this becomes impractical. We could exclude >> those reflections in the map only, but they will have been used in density >> modification so they are no longer truly free. I don't have a good >> solution for that. >> >> I am guessing that for model-building, the free R is hardly affected, >> compared to refinement against the map, though I haven't tested this. >> >> All the best, >> Tom T >> >>>> Hi Joe, hi Tom, >>>> >>>> until recently, all reflections (work and test) were used in map >>>> calculation. When I added a real-space refinement option to >>>> phenix.refine I spent a day thinking hard about why Rfree was almost >>>> always equal to Rwork after real-space refinement, until I realized >>>> that >>>> I have to exclude test reflections from map calculation, and that fixed >>>> the problem. >>>> >>>> I think it depends on the task: >>>> >>>> - for things like real-space refinement (where the map is heavily used) >>>> or automated model building, the test reflections have to be excluded >>>> from map calculation; >>>> >>>> - for catching a tiny detail (looking at weak ligand density = slight >>>> map use) or fixing a few side chains, all reflections should be used, >>>> since 10% of data put aside may sometime significantly affect map >>>> quality. >>>> >>>> Pavel. >>>> >>>> >>>> On 9/30/09 11:51 AM, Tom Terwilliger wrote: >>>>> Hi Joe, >>>>> In PHENIX R-free reflections are included in your maps. >>>>> All the best, >>>>> Tom T >>>>> >>>>> On Sep 30, 2009, at 12:47 PM, Joe Krahn wrote: >>>>> >>>>>> Does PHENIX exclude R-free reflections when computing maps? IMHO, it >>>>>> is >>>>>> bad to use test reflections in maps, or anywhere else other than >>>>>> computing R-free, but opinions vary. If some people still want test >>>>>> reflections in maps, maybe it could be an option. >>>>>> >>>>>> Thanks, >>>>>> Joe Krahn >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >> >>

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Re: [phenixbb] FreeR set reduced by half in twin crystal refinement?
by lauren 08 Oct '09

08 Oct '09

Hi all Thanks for all your reply, really helpful Joe wrote, >My first guess is that the R-free set generated in CCP4 is not set to follow twin laws, so you have work and free reflections associated by twinning. However, I would expect PHENIX >to check this. >As for the reduced size, that probably comes from the way the twinned test set is calculated. Maybe it is a bug. Are you using anomalous data? No anomalous >What is the PHENIX version? Peter wrote, >- you have at least n% of free flags, but not more then 2000+epsilon >(typically) >- it follows any possible twin law (not user specified, it follows symmetry of the lattice) After I change the setting "xray_data.r_free_flags.max_free ", and set it up to 5000. xray_data.r_free_flags.fraction=0.05, the results look normal. Final: r_work = 0.1782 r_free = 0.2285 bonds = 0.007 angles = 1.186 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1807 REMARK 3 R VALUE (WORKING SET) : 0.1782 REMARK 3 FREE R VALUE : 0.2285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.07 REMARK 3 FREE R VALUE TEST SET COUNT : 2776 Best Regards Lauren

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parallel phaser?
by Francis E Reyes 07 Oct '09

07 Oct '09

Did phaser get OpenMP/parallelized or was I just having a dream? If so, how's it work? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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FreeR set reduced by half in twin crystal refinement?
by lauren 07 Oct '09

07 Oct '09

Hi everyone, I have a P31 twin crystal, resolution 2.0, and with twin fraction 0.451. I use phenix.refine to refine the structure and with freeR set to 8%. % phenix.refine data.sca model.pdb twin_law="h,-h-k,-l" xray_data.r_free_flags.generate=True xray_data.r_free_flags.fraction=0.08 Result: Final: r_work = 0.1793 r_free = 0.2258 bonds = 0.011 angles = 1.557 REMARK 3 FREE R VALUE : 0.2258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.67 REMARK 3 FREE R VALUE TEST SET COUNT : 2013 After the refinement, it seems like my freeR set size reduced by half (3.67%). Is it due to the twin effect, or something is wrong with my refinement? And if I use ccp4 program "scalpeak2mtz " to convert the .sca to .mtz and with freeR fraction set to 8%. Then refine it with phenix. % phenix.refine data.mtz model.pdb twin_law="h,-h-k,-l" Final: r_work = 0.1669 r_free = 0.1970 bonds = 0.010 angles = 1.406 REMARK 3 FREE R VALUE : 0.2022 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.80 REMARK 3 FREE R VALUE TEST SET COUNT : 4326 It turns out, my test set is still 8%, and R/Rfree looks even better than the first one. So I am wondering which one is the correct one and why? Thanks! Lauren

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difference map peaks
by RAVINDRA D MAKDE 07 Oct '09

07 Oct '09

Hi everyone, I would like to have commnets from experts on the following issues. I am refining DNA-protein complex at 3 A resolution and my current Rfree is 21.5 % (phenix.refine). 1. I am getting difference map peaks (in Coot) of magnitude less than -5 sigmas (0.24 e/A3) (~10 or more peaks) and equal number of positive peaks of same magnitudes.The positive peaks hardly have 2fo-fc of more than 1.0 sigma level. I presumed this well could be due to bulk solvent or improper mask. Therefore I optimized the mask parameters (by giving option under "General refinement parameters" in phenix.refine GUI). I could get my R free lower as expected but I still got these peaks back. Although I am not absolutely sure, but positive peaks are more in polar pocket of protein and negative peaks are more in non-polar and aromatic pockets. I have PEG, Na acetate in my crystal soup. What these negative peaks represent for? 2. During addition of atoms like Na+, Cl- in map, do one need to careful about of the its coordination valency in surrounding pocket. ? I will be highly thankful to you for the same. Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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prime_and_switch, error in input mtz label assignment
by Tatyana Sysoeva 06 Oct '09

06 Oct '09

Dear all, I have a question to your kindest attention. We were trying to run today phenix on distant cluster (phenix-1.3) with next command line *phenix.autobuild data=data.mtz solvent_fraction=0.6 ps_in_rebuild=True \ input_pdb_file=model.pdb maps_only=True* Autobuild failed with these last lines in the Autobuild_run_1_1.log Failed to carry out AutoBuild_multiple_models: *Sorry, subprocess failed...message is: ******************************************************************************** phenix.autobuild \ write_run_directory_to_file=/home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/AutoBuild_run_1_/TEMP0/INFO_FILE_1 Reading effective parameters from /home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/AutoBuild_run_1_/TEMP0/PARAMS_1.eff Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** * in Autobuild_run_1_/TEMP0/Autobuild_run_1_/Autobuold_run_1_1.log the failure message is next: *Columns of data in AutoBuild_run_1_/TEMP0/TEMP.mtz: H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT child process stderr output: command: 'AutoBuild_run_1_/TEMP0/temporary.com' resolve_giant: Error in label assignments Failed to run resolve ---------------------------------- TRIED resolve_giant ...but not OK ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** * There are temporary.com and temporary.com.bak in the folder and there is only difference, except that in temporary.com there is "labin FP=FP FC=FMODEL PHIC=PH2FOFCWT FWT=2FOFCWT" in temporary.com.bak there is "labin FP=FP FC=FMODEL PHIC=PHI2FOFCWT FWT=2FOFCWT" Prime_and_switch.log file ends with *Reading SG information from TEMP.mtz Space group name: P21212 Point group: 222 Space group number : 18 Symmetry operators: 4 Number of columns: 9 H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT *** Warning From LRASSN : User input label PHI2FOFCWT does not match any file label  resolve_giant: Error in label assignments </pre>   </html> * I checked created TEMP.mtz, it looks like: * Column Labels : H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT So the question is next: Why is prime_and_switch process looking for the "right" labels (PH2FOFCWT), which are present in previously created TEMP.mtz file, but sees them wrong (PHI2FOFCWT)? Is this possible that we have somewhat wrong inputs or is there problem with the set of commands? Sincerely, Tanya * *

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log file
by Young-Jin Cho 06 Oct '09

06 Oct '09

Hi, While I refining I found the following is included in the .log file. I am using different pdb files. When I looked up residue number 175, it looked ok to me. Do you guys have any idea how to deal with this? Conformer: "C" Number of residues, atoms: 175, 1321 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 159, 'PCIS': 1} Chain breaks: 24 Unresolved chain link angles: 14 Unresolved chain link dihedrals: 28 Unresolved chain link planarities: 14 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1313 Thanks in advance, Young-Jin

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PHENIX 1.5 and exploding residues
by Antony Oliver 06 Oct '09

06 Oct '09

Dear all, I am currently refining a structure using PHENIX 1.5-3 and have encountered some problems with "exploding residues". I have attached a image (small PNG file) highlighting the problem. Has anyone had a similar experience? Or know the solution to the problem? Change weighting in favour of geometry ? Many thanks, Tony Oliver . The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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question about constrain ncs
by crystallogrphy 06 Oct '09

06 Oct '09

Hi, I am refining a 3.6A data set. There are 5 monomers per asymetric unit. I am considering to use constrained NCS to increase the ratio of reflection/parameter. Does phenix.refine has a script to put contrained ncs or I just use simple_ncs_from_pdb to determine the best NCS?

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Latest phenix from command line
by Graeme Winter 05 Oct '09

05 Oct '09

Hi Folks, I'm one of those people who use the command-line for everything, and I just found my "phenix mad spell" phenix.autosol sites=8 atom_type=Se infl.data=TS03_12287_free.mtz \ infl.f_prime=-9.9 infl.f_double_prime=3.9 low.data=TS03_12287_free.mtz \ low.f_prime=-3.3 low.f_double_prime=0.5 \ infl.labels='F_INFL SIGF_INFL DANO_INFL SIGDANO_INFL' \ low.labels='F_LREM SIGF_LREM DANO_LREM SIGDANO_LREM' no longer appears to work: Traceback (most recent call last): File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 585, in <module> run_autosol=run_autosol(args=sys.argv[1:]) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 300, in __init__ self.Sorry(line) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 1238, in Sorry raise AssertionError,e AssertionError: Sorry, unknown file or keyword: infl.data=TS03_12287_free.mtz Possibilities... (use 'phenix.autosol --help all' to get full help): general.data_quality=TS03_12287_free.mtz data=TS03_12287_free.mtz Looked at the doc and saw: MAD dataset The inputs for a MAD dataset need to specify f_prime and f_double_prime for each wavelength. You can use a parameters file "mad.eff" to input MAD data. You run it with "phenix.autosol mad.eff". Here is an example of a parameters file for a MAD dataset. You can set many additional parameters as well (see the list at the end of this document). autosol { seq_file = seq.dat sites = 2 atom_type = Se wavelength { data = peak.sca lambda = .9798 f_prime = -8.0 f_double_prime = 4.5 } wavelength { data = inf.sca lambda = .9792 f_prime = -9.0 f_double_prime = 1.5 } So I make mad.eff from information above, then -bash-3.2$ phenix.autosol mad.eff Traceback (most recent call last): File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 585, in <module> run_autosol=run_autosol(args=sys.argv[1:]) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 155, in __init__ self.process_wizard_params(args) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 562, in process_wizard_params self.Sorry("Unrecognized file or keyword: "+str(arg)) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 1238, in Sorry raise AssertionError,e AssertionError: Unrecognized file or keyword: mad.eff As listed in the instructions. Any clues, anyone? Many thanks in advance, Graeme

2 2

PHENIX parallel computing?
by Joe Krahn 03 Oct '09

03 Oct '09

A parallel version of PHENIX was discussed before. I know that parallelization of refinement is difficult, and probably not worth the effort when there is still a lot of function/methods work. However, running parallel independent tasks could pay off without a lot of work. For example, optimization of WXU and WXC can spawn multiple tasks with different test weights. Annealing tasks could also run multiple jobs, and pick the best result, or even merge results based on real-space fit analysis. Joe Krahn

2 1

Does PHENIX exclude Rfree reflections in maps?
by Joe Krahn 02 Oct '09

02 Oct '09

Does PHENIX exclude R-free reflections when computing maps? IMHO, it is bad to use test reflections in maps, or anywhere else other than computing R-free, but opinions vary. If some people still want test reflections in maps, maybe it could be an option. Thanks, Joe Krahn

8 11

installing phenix 1.5-2
by Tirumala Kumar Chowdary 02 Oct '09

02 Oct '09

Hi, My 1.5-2 build installation is failing with this error 'installing binary components making directory build-binary/intel-linux-2.6-x86_64/beryl/tmp/binary gzip: /nfs/home/chowdary/Download/phenix-installer-1.5-2/bundles/bundle-1.5-2-intel-linux-2.6-x86_64.tar.gz: invalid compressed data--format violated finding installed versions finding binary versions cat: build/intel-linux-2.6-x86_64/version: No such file or directory no pre-existing binary components detected installing new binary package configuring PHENIX components Error configuring: see /nfs/home/chowdary/Download/phenix-installer-1.5-2/build-binary/intel-linux-2.6-x86_64/beryl/log/binary.log for details' and the log file shows this error. /bin/tar: Unexpected EOF in archive /bin/tar: Unexpected EOF in archive /bin/tar: Error is not recoverable: exiting now /nfs/home/chowdary/Download/phenix-installer-1.5-2/bin/install-from-binary: line 349: /nfs/home/chowdary/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/bin/python: No such file or directory. Earlier builds (1.4.175) are installing and running fine on the same machine. Help please.. Tirumal

2 1

RESOLVE question
by Peter Grey 01 Oct '09

01 Oct '09

Hello, We use iterative cycles of manual building (coot) - refinement (phenix) - density modification to improve maps for the next building step (RESOLVE). Should we use FMODEL,PHIFMODEL from phenix or FCALC,PHIFCALC in the input to RESOLVE. MODEL structure factors are closer to experimental ones but are they better for density modification purposes ? I think that if the program uses , as in DM, only Fobs and phases to calculate the maps then PHIFCALC is better (no contribution of solvent) but if the programs calculates 2Fo-Fc maps then FMODEL,PHIFMODEL is better since it was shown that these maps are beter when bulk solvent correction is used. Could you please comment whether this reasoning is correct and give information as to which is the case in resolve. Thanks, -- Peter

2 2

Re: [phenixbb] refining sugars
by Jose M Casasnovas 01 Oct '09

01 Oct '09

Dear Ralf. I just solved the problem with the sugar refinement. Somehow the way the BETA1-4 cif defines the link is in the reverse order to the NAG-ASN cif link (at least to way I was used to do it). In the NAG-ASN cif, residue_selection_1 in the phenix.refine input must be the NAG and residue_selection_2 the ASN, such as I was used to do in CNS. However, the BETA1-4 cifs follows the opposite way: residue_selection_1 must be the first sugar residue (linked through O4) and residue_selection_2 the second sugar (linked through the C1), which is the most distant residue to the Asn. Thanks so much for your help and to all who sent comments and suggestions. Jose M Casasnovas -- Centro Nacional de Biotecnología (lab. B16) CSIC, Campus UAM Darwin 3 28049 Madrid Spain Ph. 34 915854917(8) Fax. 34 915854506 email: jcasasnovas(a)cnb.csic.es

2 1

Re: [phenixbb] refining sugars
by Engin Ozkan 30 Sep '09

30 Sep '09

I just answered Jose's question on this yesterday. The reason you are having trouble is that there is no NAG-NAG link. It is a BETA1-4. Read the post to see what data_link names are allowed, and use them for your sugars. Below is a copy-paste of my post from yesterday: >That's because there is no such data link as NAG-NAG-B-D. Instead, you >should use a BETA1-4 link. This is similar to what CNS used, if you are >familiar with that (I think it was B14 in CNS). >If you want to know where all the phenix link definitions are, type > >phenix.where_mon_lib_list_cif > >and read the file that's listed. > >It is good to read this to know which residue selection is selection_1 >and which is selection_2. In it you'll see this or something like this. > >data_link_BETA1-4 ># >loop_ >_chem_link_bond.link_id >_chem_link_bond.atom_1_comp_id >_chem_link_bond.atom_id_1 >_chem_link_bond.atom_2_comp_id >_chem_link_bond.atom_id_2 >_chem_link_bond.type >_chem_link_bond.value_dist >_chem_link_bond.value_dist_esd > BETA1-4 1 O4 2 C1 single 1.439 0.020 >loop_ >_chem_link_angle.link_id >_chem_link_angle.atom_1_comp_id >_chem_link_angle.atom_id_1 >_chem_link_angle.atom_2_comp_id >_chem_link_angle.atom_id_2 >_chem_link_angle.atom_3_comp_id >_chem_link_angle.atom_id_3 >_chem_link_angle.value_angle >_chem_link_angle.value_angle_esd > BETA1-4 1 C4 1 O4 2 C1 108.700 3.000 > BETA1-4 1 O4 2 C1 2 O5 112.300 3.000 > BETA1-4 1 O4 2 C1 2 C2 109.470 3.000 > BETA1-4 1 O4 2 C1 2 H1 109.470 3.000 >loop_ >_chem_link_tor.link_id >_chem_link_tor.id >_chem_link_tor.atom_1_comp_id >_chem_link_tor.atom_id_1 >_chem_link_tor.atom_2_comp_id >_chem_link_tor.atom_id_2 >_chem_link_tor.atom_3_comp_id >_chem_link_tor.atom_id_3 >_chem_link_tor.atom_4_comp_id >_chem_link_tor.atom_id_4 >_chem_link_tor.value_angle >_chem_link_tor.value_angle_esd >_chem_link_tor.period > BETA1-4 BETA_1 1 O4 2 C1 2 C2 2 C3 0.00 20.0 1 > BETA1-4 BETA_2 1 C4 1 O4 2 C1 2 C2 0.00 20.0 1 > BETA1-4 BETA_3 1 C3 1 C4 1 O4 2 C1 0.00 20.0 1 >loop_ >_chem_link_chir.link_id >_chem_link_chir.atom_centre_comp_id >_chem_link_chir.atom_id_centre >_chem_link_chir.atom_1_comp_id >_chem_link_chir.atom_id_1 >_chem_link_chir.atom_2_comp_id >_chem_link_chir.atom_id_2 >_chem_link_chir.atom_3_comp_id >_chem_link_chir.atom_id_3 >_chem_link_chir.volume_sign > BETA1-4 2 C1 1 O4 2 O5 2 C2 positiv > >Engin On 9/30/09 10:56 AM, Tirumala Kumar Chowdary wrote: > Thanks for the reply, > > here is part of the log file, which shows the parameter input for nag > refinement > > > Monomer Library directory: > "/usr/local/phenix/phenix-1.4-125/chem_data/mon_lib" > Total number of atoms: 6260 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1670 > residue_selection_2: chain A and resname ASN and resid 670 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain A and resname ASN and resid 784 > apply_cif_link: > data_link: NAG-NAG > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain C and resname NAG and resid 1785 > Number of models: 1 > Model: "" > Number of chains: 3 > Chain: "A" > Number of atoms: 5125 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 681, 5125 > > I am presuming that it read what ever it needs to make the ASN-NAG > bonds and NAG-NAG bonds. > > what am I missing here ? > > Tirumal > > > Quoting Engin Ozkan<eozkan(a)stanford.edu>: > >> You don't need to create cif files; phenix has them. NAG is definitely >> there, and you can have two NAGs linked by any biologically-relevant >> glycosidic bond you want. You need to define the links, however. I think >> posting the cif_link.params may get you more help. >> >> Engin >> >> On 9/30/09 8:49 AM, Tirumala Kumar Chowdary wrote: >>> Hi, >>> >>> My question is related to the 'refining sugars in phenix' questions >>> that have been appearing on the bb for the last two days. >>> >>> I am trying to refine my NAGs and somehow phenix is ignoring the sugars >>> in my structure. Neither it is making a bond between my ASN and NAG nor >>> NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, >>> though. >>> >>> I am using in version 1.4.125 still. Is this the problem ? Does >>> upgrading to any of the later build will help ? >>> >>> >>> Tirumal >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> -- >> Engin Özkan >> Post-doctoral Scholar >> Howard Hughes Medical Institute >> Dept of Molecular and Cellular Physiology >> 279 Campus Drive, Beckman Center B173 >> Stanford School of Medicine >> Stanford, CA 94305 >> ph: (650)-498-7111 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

1 0

GUI fonts
by Frank von Delft 30 Sep '09

30 Sep '09

Hi, I've just been poking around the new GUIs - neat!! But the font is absolutely enormous, which is terrifically annoying. Where do I change it? (I didn't see it in the preferences.) Cheers phx

2 2

refining sugars
by Tirumala Kumar Chowdary 30 Sep '09

30 Sep '09

Hi, My question is related to the 'refining sugars in phenix' questions that have been appearing on the bb for the last two days. I am trying to refine my NAGs and somehow phenix is ignoring the sugars in my structure. Neither it is making a bond between my ASN and NAG nor NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, though. I am using in version 1.4.125 still. Is this the problem ? Does upgrading to any of the later build will help ? Tirumal

4 3

N-linked glycans in phenix.refine
by Jose Casasnovas 30 Sep '09

30 Sep '09

Dear Phenix users. I am trying to refine N-linked glycans in phenix. The Asn-NAG link appears to be recognize by the program, but the NAG-NAG link is not. I guess the cif_link must be missing. Monomer Library directory: "/home/soft/phenix/phenix-1.4-3/ext_ref_files/mon_lib" Total number of atoms: 8947 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain N and resname NAG and resid 5161 residue_selection_2: chain E and resname ASN and resid 516 apply_cif_link: data_link: NAG-NAG-B-D Sorry: Missing CIF link: data_link_NAG-NAG-B-D Please check for spelling errors or specify the file name with the link as an additional argument. How can I get the required cif_link file and where to place it?? Any suggestion. Thanks. Jose

3 4

Phenix version 1.5 Released
by Paul Adams 29 Sep '09

29 Sep '09

The Phenix developers are pleased to announce that version 1.5 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.5-2) are: - A new Graphical User Interface (accessed by typing phenix at the command line) - Two-way communication with Coot - The latest version of Phaser (2.2) - A development version of torsion angle dynamics available in phenix.refine - Real space refinement in phenix.refine - New GUIs for Autosol, AutoBuild and LigandFit wizards - A number of MolProbity and other validation tools now available - Fast loop building with phenix.fit_loops - Improved ligand geometry generation with phenix.elbow - Inclusion of Nicholas Sauter's LABELIT system for autoindexing and more For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

1 0

anomalous difference map demonstration in pymol
by crystallogrphy 29 Sep '09

29 Sep '09

Hi, I have used anomalous data to do refinement. The crystal diffracts to 3.5A. The resulting mtz file shows good anomalous density around the heavy atoms. Now I want to demonstrate the density in Pymol. Does anyone know how to generate the map use the map file in MTZ format in Pymol? Thanks!

3 2

transfering R-free flags
by Tirumala Kumar Chowdary 28 Sep '09

28 Sep '09

Hi, I am trying to refine my model against a higher resolution file. I want to transfer my R-free flags generated by phenix.refine from the lower resolution mtz to the higher resolution file. Is there a way to transfer the R-free flags in Phenix ? If not, where can I find the mtz file from my earlier refinement with R-free flags generated ? Does phenix.refine generate this file and save it for me somewhere ? Thanks Tirumal

2 1

NCS restraints with TLS
by Joe Krahn 28 Sep '09

28 Sep '09

I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct? In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less. I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common. Joe Krahn

6 8

NCS averaged maps?
by Francis E Reyes 26 Sep '09

26 Sep '09

With all the recent talk about kicked and filled maps, can we have phenix output an ncs averaged map for those of us who have NCS? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

1 0

extend R-free set to higher resolution
by NATHAN THOMSEN 25 Sep '09

25 Sep '09

Is there a phenix utility to extend a phenix generated R-free set to higher resolution (while still using lattice symmetry etc.)? Thanks! Nathan Thomsen UC Berkeley

2 1

Re: [phenixbb] extend R-free set to higher resolution
by Thomas C. Terwilliger 25 Sep '09

25 Sep '09

Hi Nathan, Yes, you can use the GUI to do this (you need a recent nightly build to do it). Just click on "Reflection file editor" and you get an option to extend a free R set, maintaining the free R set you already have. All the best, Tom T >> Is there a phenix utility to extend a phenix generated R-free set to >> higher resolution (while still using lattice symmetry etc.)? Thanks! >> >> Nathan Thomsen >> UC Berkeley >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

1 0

wxu_scale is ignored with TLS
by Joe Krahn 25 Sep '09

25 Sep '09

When using TLS, the wxu_scale is changed, even if it is given in the input file. IMHO, TLS should only modify the default value, and not a user-defined wxu_scale. Thanks, Joe Krahn

3 3

Various problems with phenix.refine
by Joe Krahn 25 Sep '09

25 Sep '09

Here are a few problems I have found using phenix.refine 1.4: If NCS restraint selection in the .def file have newline characters, the REMARK 3 formatting is messed up. It should probably replace all white-space regions with a single space. When NCS restraints contain a residue with alternate conformations, that residue gets excluded from all equivalences, even if the selections contain ALTID to avoid the redundant atoms. If the .def file has a syntax error, phenix.refine dies with an error that the file format is not recognized. Why not print syntax errors? The optimize_wxc and optimize_wxu features are useful, but it is difficult to use the result to define an improved fixed scale on subsequent rounds, without having to optimize every time. It is not obvious whether the scale written in the log represents the new wxc_scale, or if it is a multiplier versus the current wxc_scale. The log also truncates to 2 decimal places. In my case, I only get one significant digit from scale=0.05. I propose that the optimizations write something like "Optimal wxc_scale = 0.533". The input data is written as "refine_data.mtz", not using the serial number, and there seems to be no flag to disable writing it. That means I have to force overwrite to run iterations in the same directory. If each run is in its own directory, the serial number is not very useful for filenames. So, the output MTZ should have the serial number, and you might also consider an option to disable the serial number when separate directories are used. Thanks, Joe Krahn

4 5

specifying column labels for input MTZ file
by Tirumala Kumar Chowdary 24 Sep '09

24 Sep '09

Hi, I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). Phenix.refine stopped at 'Multiple equally suitable arrays of observed xray data found. Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav Please use refinement.input.xray_data.labels' Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it. Thanks Tirumal

15 26

question about rfree flag transfer
by crystallogrphy 23 Sep '09

23 Sep '09

Hi, I have built a model against a 3.7A data set by AutoBuild. The resulting model is overall_best.pdb. The data with the rfree test flags is exptl_fobs_phases_freeR_flags.mtz Later on, I got a 3.4A data, which is isomorphous with the 3.7A data. Now I want to transfer the rfree flag from the 3.7A to 3.4A data for refinement. I know one strategy if the data file is in CNS format. That is, use DATAMAN to transfer the flags and generate new test set flags in the high resolution range: 3.7-3.4A. However, when I convert the format by phenix.reflection_file_converter, it fails: phenix.reflection_file_converter exptl_fobs_phases_freeR_flags.mtz --cns=exptl_fobs_phases_freeR_flags.cv --label="PHIM" --label="FP,SIGFP" --label="FOMM" --label="FreeR_flag" --label="FC" However, the resulting data does not have any FP, SIGFP, and FreeR flags. { file: exptl_fobs_phases_freeR_flags.cv.cns } { sg=C2 a=175.385 b=102.472 c=92.057 alpha=90 beta=111.312 gamma=90 } { source of data: exptl_fobs_phases_freeR_flags.mtz:FC } NREFlections=15307 ANOMalous=FALSe DECLare NAME=DATA DOMAin=RECIprocal TYPE=REAL END INDEx 0 0 5 DATA= 0 INDEx 0 0 7 DATA= 0 INDEx 0 0 8 DATA= 0 INDEx 0 0 9 DATA= 0 INDEx 0 0 10 DATA= 0 INDEx 0 0 11 DATA= 0 INDEx 0 0 12 DATA= 0 INDEx 0 0 13 DATA= 0 I also tried mtz2various in CCP4i, the resulting hkl file does not have rfree flags at all. Does anyone know who to convert the exptl_fobs_phases_freeR_flags.mtz into cns format or simple transfer the flags by phenix?

2 1

supported compilers for source builds
by Ben Eisenbraun 22 Sep '09

22 Sep '09

For compiling PHENIX from source, what are the supported compilers? Are the Intel or Portland compilers supported? There are notes in the list archives about using OpenMP with gcc, and hints that the Intel compiler is supported, but I didn't see any docs on building with icc/ifort. In one email Ralf mentions that you might actually lose performance compiling your own version of Solve/Resolve because gfortran optimizes poorly, which leads me to think that the distributed binaries are using ifort for at least the Solve/Resolve bits. Did I overlook some notes on how to do this? -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

2 3

question about composite SA_omit map in phenix
by crystallogrphy 22 Sep '09

22 Sep '09

Hi, I am using molecular replacement to build a model against a 2.2A resolution data set. However, the template model only has 23% sequence identity. First, I use chainsaw in CCP4i to prune all side chain to be poly-Ala except the identical residues. Then I use AutoMR and rigid body refinement, I got Rfree=50%. The continuous electron density is not bad showing second structures. However, the model has some out-of-registration problem, for example, two proline are in a alpha-helix. In other words, it has model bias. I want to use composite SA-omit to get a less model bias map, not a simple composite omit map or a SA_omit map ommiting a part of the region. Does someone know who to do this? Thanks! Qun Wan postdoc fellow Case Western Reserve University

10 19

heavy atom in pdb for refinement
by crystallogrphy 20 Sep '09

20 Sep '09

Hi, I have Zn atoms in my pdb for refinement. However, it failed with the following scripts. Do I have to create a libary of this heavy atom? Number of atoms with unknown nonbonded energy type symbols: 6 "ATOM 1 Zn Zn Z 1 .*. Zn " "ATOM 2 Zn Zn Z 2 .*. Zn " "ATOM 3 Zn Zn Z 3 .*. Zn " "ATOM 4 Zn Zn Z 4 .*. Zn " "ATOM 5 Zn Zn Z 5 .*. Zn " "ATOM 6 Zn Zn Z 6 .*. Zn " Time building chain proxies: 1.78, per 1000 atoms: 0.45 Here is the format of my pdb: ..... ATOM 1 Zn Zn Z 1 32.028 47.603 13.955 1.00 30.00 Zn ATOM 2 Zn Zn Z 2 29.017 71.434 8.164 1.00 30.00 Zn ATOM 3 Zn Zn Z 3 39.223 49.330 -6.810 1.00 30.00 Zn ATOM 4 Zn Zn Z 4 24.811 89.144 -4.406 1.00 30.00 Zn ATOM 5 Zn Zn Z 5 23.652 72.429 6.125 1.00 30.00 Zn ATOM 6 Zn Zn Z 6 30.132 63.054 -31.918 1.00 30.00 Zn TER 7 Zn 6 ATOM 10 CL CL L 1 20.125 63.405 10.719 1.00 30.00 CL TER 11 CL 1

5 7

RuntimeError : min()
by RAVINDRA D MAKDE 19 Sep '09

19 Sep '09

Hi all, I will highly appreciate your help to resolve the following bugs encountered during running phenix.refine on GUI as well as on command lines. My version of Phenix and platform are: PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 3 cctbx tag: 2008_12_07_1353 Platform: mac-intel-osx osx-10.5.8 The error encountered using phenix refinement GUI (phenix.refine_gui) is as follows: A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks!RuntimeError : min() argument is an empty arrayTraceback:Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Base.py", line 274, in OnBrowse self.file_text_field.SetValue(new_path) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Controls.py", line 974, in SetValue self.phil_handler.propagate_update(self.phil_def_name, new_value) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/PhilInterfaceHandler.py", line 103, in propagate_update self._update_handlers[def_name](self, def_name, value) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Extensions.py", line 28, in extract_xray_neutron_params phil_def_name = phil_object_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 155, in __init__ self.load_reflection_file(file_name, phil_def_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 159, in load_reflection_file self.hkl_server = self.hkl_handler.add_hkl_file(file_name, phil_def_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 66, in add_hkl_file err=sys.stderr) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0): The error encountered using phenix refinement on command line (phenix.refine coordinate.pdb reflection.mtz) is as follows: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0):RuntimeError: min() argument is an empty array N.B. Earlier, I had encountered the similar error (using command line) using PHENIX version 1.3 on the same platform. Thanks in advance. Regards, Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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Re: [phenixbb] xtriage to double-check symmetry
by Frank von Delft 18 Sep '09

18 Sep '09

>>>> >>>> So I thought I'd listen to xtriage: seemed easy since I have both >>>> data >>>> and model in P6522, and I ran: >>>> phenix.xtriage final.mtz reference.structure.file=final.pdb >>>> > Uh-oh.... what I meant is, I have both data and model in ==>P65<==. (Bad typo -- explains Peter's patient but puzzled response, which did however confirm I'd understood correctly after all :) So, again: I have *some* lower symmetry (not P1, though); should I expect xtriage to print out tests for P6522 somewhere? Because I don't find it. <later> That said: after updating phenix to 1.4-162, I now do find that table in the output (attached, last table), and it seems we're in-between: seems we have probably indeed missed the two-fold, so now we must figure out why it "didn't refine" in P6522. Thanks for you help and explanation! phx. > But isn't P6522 already the highest symmetry? I think if you run X-triage > on the data reduced as P65, it will as you say check the extra operations > implied by p6522 and see if they are justified. > If the data is already reduced in p6522, those reflections have already > been merged and there is no way to tell how good the agreement was? > > I don't think xtriage will look at your model- but then I've never > given it a model. > I would guess from your lower Rfree in P65 that it is the lower symmetry- > the 2-fold operators that make it almost fit p6522 are psuedosymmetry, > noncrystallographic symmetry that almost fits the p6522 operators but > not quite. > > Best, > Ed ############################################################# ## phenix.xtriage ## ## ## ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## ## ## ############################################################# #phil __OFF__ Date 2009-09-18 Time 08:19:32 BST +0100 (1253258372.97 s) ##-------------------------------------------## ## WARNING: ## ## Number of residues unspecified ## ##-------------------------------------------## Effective parameters: #phil __ON__ scaling { input { asu_contents { n_residues = None n_bases = None n_copies_per_asu = None } xray_data { file_name = "final.mtz" obs_labels = None calc_labels = None unit_cell = 81.38990021 81.38990021 79.47530365 90 90 120 space_group = "P 65" high_resolution = None low_resolution = None reference { data { file_name = None labels = None unit_cell = None space_group = None } structure { file_name = "final.pdb" } } } parameters { reporting { verbose = 1 log = "logfile.log" ccp4_style_graphs = True } misc_twin_parameters { missing_symmetry { sigma_inflation = 1.25 } twinning_with_ncs { perform_analyses = False n_bins = 7 } twin_test_cuts { low_resolution = 10 high_resolution = None isigi_cut = 3 completeness_cut = 0.85 } } } optional { hklout = None hklout_type = mtz sca *mtz_or_sca label_extension = "massaged" aniso { action = *remove_aniso None final_b = *eigen_min eigen_mean user_b_iso b_iso = None } outlier { action = *extreme basic beamstop None parameters { basic_wilson { level = 1e-06 } extreme_wilson { level = 0.01 } beamstop { level = 0.001 d_min = 10 } } } symmetry { action = detwin twin *None twinning_parameters { twin_law = None fraction = None } } } } gui { result_file = None } } #phil __END__ Symmetry, cell and reflection file content summary Miller array info: final.mtz:F,SIGF Observation type: xray.amplitude Type of data: double, size=15235 Type of sigmas: double, size=15235 Number of Miller indices: 15235 Anomalous flag: False Unit cell: (81.3899, 81.3899, 79.4753, 90, 90, 120) Space group: P 65 (No. 170) Systematic absences: 0 Centric reflections: 606 Resolution range: 35.2429 2.20034 Completeness in resolution range: 0.999344 Completeness with d_max=infinity: 0.999082 ##----------------------------------------------------## ## Basic statistics ## ##----------------------------------------------------## Matthews coefficient and Solvent content statistics Number of residues unknown, assuming 50% solvent content ---------------------------------------------------------------- | Best guess : 278 residues in the asu | ---------------------------------------------------------------- Completeness and data strength analyses The following table lists the completeness in various resolution ranges, after applying a I/sigI cut. Miller indices for which individual I/sigI values are larger than the value specified in the top row of the table, are retained, while other intensities are discarded. The resulting completeness profiles are an indication of the strength of the data. ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 35.25 - 5.42 | 99.9% | 98.8% | 97.7% | 96.5% | 94.7% | 92.0% | | 5.42 - 4.30 | 100.0% | 99.1% | 97.9% | 97.1% | 94.6% | 91.8% | | 4.30 - 3.76 | 100.0% | 99.3% | 98.0% | 96.6% | 93.4% | 89.4% | | 3.76 - 3.42 | 100.0% | 98.9% | 96.2% | 93.5% | 87.1% | 80.7% | | 3.42 - 3.17 | 100.0% | 95.2% | 91.3% | 87.4% | 76.8% | 62.0% | | 3.17 - 2.99 | 100.0% | 93.7% | 86.3% | 76.9% | 60.7% | 45.2% | | 2.99 - 2.84 | 100.0% | 88.3% | 73.8% | 60.3% | 37.7% | 19.2% | | 2.84 - 2.71 | 100.0% | 83.5% | 66.6% | 50.2% | 24.2% | 11.4% | | 2.71 - 2.61 | 100.0% | 75.9% | 55.7% | 41.2% | 18.0% | 6.9% | | 2.61 - 2.52 | 99.9% | 69.8% | 44.4% | 28.7% | 10.9% | 5.2% | | 2.52 - 2.44 | 99.5% | 61.0% | 34.9% | 19.6% | 8.2% | 3.9% | | 2.44 - 2.37 | 98.6% | 57.6% | 28.8% | 15.8% | 5.8% | 2.6% | | 2.37 - 2.31 | 98.8% | 44.3% | 20.0% | 11.2% | 4.7% | 2.0% | | 2.31 - 2.25 | 99.2% | 31.5% | 14.4% | 7.6% | 3.4% | 0.8% | ---------------------------------------------------------------------------------------- The completeness of data for which I/sig(I)>3.00, exceeds 85% for resolution ranges lower than 2.99A. The data are cut at this resolution for the potential twin tests and intensity statistics. Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of None: 49.24 A**(-2) Estimated -log of scale factor of None: 0.40 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of None: 51.68, -0.00, 0.00 51.68, -0.00 44.95 Equivalent representation as U_cif: 0.65, 0.33, -0.00 0.65, 0.00 0.57 Eigen analyses of B-cart: Value Vector Eigenvector 1 : 51.675 ( 0.91, -0.42, 0.00) Eigenvector 2 : 51.675 ( 0.42, 0.91, -0.00) Eigenvector 3 : 44.948 (-0.00, 0.00, 1.00) ML estimate of -log of scale factor of None: 0.40 Correcting for anisotropy in the data Some basic intensity statistics follow. Low resolution completeness analyses The following table shows the completeness of the data to 5 Angstrom. unused: - 35.2437 [ 0/4 ] 0.000 bin 1: 35.2437 - 10.6916 [138/139] 0.993 bin 2: 10.6916 - 8.5258 [136/136] 1.000 bin 3: 8.5258 - 7.4597 [127/127] 1.000 bin 4: 7.4597 - 6.7830 [133/133] 1.000 bin 5: 6.7830 - 6.2998 [133/133] 1.000 bin 6: 6.2998 - 5.9302 [133/133] 1.000 bin 7: 5.9302 - 5.6345 [131/131] 1.000 bin 8: 5.6345 - 5.3901 [128/128] 1.000 bin 9: 5.3901 - 5.1832 [133/133] 1.000 bin 10: 5.1832 - 5.0049 [137/137] 1.000 unused: 5.0049 - [ 0/0 ] Mean intensity analyses Analyses of the mean intensity. Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. The following resolution shells are worrisome: ------------------------------------------------ | d_spacing | z_score | compl. | <Iobs>/<Iexp> | ------------------------------------------------ | 6.201 | 5.09 | 1.00 | 0.681 | ------------------------------------------------ Possible reasons for the presence of the reported unexpected low or elevated mean intensity in a given resolution bin are : - missing overloaded or weak reflections - suboptimal data processing - satellite (ice) crystals - NCS - translational pseudo symmetry (detected elsewhere) - outliers (detected elsewhere) - ice rings (detected elsewhere) - other problems Note that the presence of abnormalities in a certain region of reciprocal space might confuse the data validation algorithm throughout a large region of reciprocal space, even though the data are acceptable in those areas. Possible outliers Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 Acentric reflections: ----------------------------------------------------------------- | d_space | H K L | |E| | p(wilson) | p(extreme) | ----------------------------------------------------------------- | 3.054 | 0, 1, 26 | 5.09 | 5.35e-12 | 7.77e-08 | ----------------------------------------------------------------- p(wilson) : 1-(1-exp[-|E|^2]) p(extreme) : 1-(1-exp[-|E|^2])^(n_acentrics) p(wilson) is the probability that an E-value of the specified value would be observed if it were selected at random the given data set. p(extreme) is the probability that the largest |E| value is larger or equal than the observed largest |E| value. Both measures can be used for outlier detection. p(extreme) takes into account the size of the dataset. Centric reflections: ----------------------------------------------------------------- | d_space | H K L | |E| | p(wilson) | p(extreme) | ----------------------------------------------------------------- | 6.408 | 0, 11, 0 | 3.81 | 1.38e-04 | 7.72e-02 | ----------------------------------------------------------------- p(wilson) : 1-(erf[|E|/sqrt(2)]) p(extreme) : 1-(erf[|E|/sqrt(2)])^(n_acentrics) p(wilson) is the probability that an E-value of the specified value would be observed when it would selected at random from the given data set. p(extreme) is the probability that the largest |E| value is larger or equal than the observed largest |E| value. Both measures can be used for outlier detection. p(extreme) takes into account the size of the dataset. Ice ring related problems The following statistics were obtained from ice-ring insensitive resolution ranges mean bin z_score : 1.55 ( rms deviation : 1.28 ) mean bin completeness : 1.00 ( rms deviation : 0.00 ) The following table shows the z-scores and completeness in ice-ring sensitive areas. Large z-scores and high completeness in these resolution ranges might be a reason to re-assess your data processsing if ice rings were present. ------------------------------------------------ | d_spacing | z_score | compl. | Rel. Ice int. | ------------------------------------------------ | 3.897 | 0.17 | 1.00 | 1.000 | | 3.669 | 2.93 | 1.00 | 0.750 | | 3.441 | 2.03 | 1.00 | 0.530 | | 2.671 | 3.02 | 1.00 | 0.170 | | 2.249 | 2.71 | 1.00 | 0.390 | ------------------------------------------------ Abnormalities in mean intensity or completeness at resolution ranges with a relative ice ring intensity lower than 0.10 will be ignored. No ice ring related problems detected. If ice rings were present, the data does not look worse at ice ring related d_spacings as compared to the rest of the data set. Basic analyses completed ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 2.99 Angstrom. Determining possible twin laws. The following twin laws have been found: -------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | -------------------------------------------------------------------------------- | M | 2-fold | 0.000 | 0.000 | 0.000 | h,-h-k,-l | -------------------------------------------------------------------------------- M: Merohedral twin law PM: Pseudomerohedral twin law 1 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 1 twin operator were found Details of automated twin law derivation ---------------------------------------- Below, the results of the coset decomposition are given. Each coset represents a single twin law, and all symmetry equivalent twin laws are given. For each coset, the operator in (x,y,z) and (h,k,l) notation are given. The direction of the axis (in fractional coordinates), the type and possible offsets are given as well. Furthermore, the result of combining a certain coset with the input space group is listed. This table can be usefull when comparing twin laws generated by xtriage with those listed in lookup tables In the table subgroup H denotes the *presumed intensity symmetry*. Group G is the symmetry of the lattice. Left cosets of : subgroup H: P 6 and group G: P 6 2 2 Coset number : 0 (all operators from H) x,y,z h,k,l Rotation: 1 ; direction: (0, 0, 0) ; screw/glide: (0,0,0) -x,-y,z -h,-k,l Rotation: 2 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) -y,x-y,z k,-h-k,l Rotation: 3 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) -x+y,-x,z -h-k,h,l Rotation: 3 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) x-y,x,z h+k,-h,l Rotation: 6 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) y,-x+y,z -k,h+k,l Rotation: 6 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) Coset number : 1 (H+coset[1] = P 6 2 2) x-y,-y,-z h,-h-k,-l Rotation: 2 ; direction: (1, 0, 0) ; screw/glide: (0,0,0) -y,-x,-z -k,-h,-l Rotation: 2 ; direction: (-1, 1, 0) ; screw/glide: (0,0,0) x,x-y,-z h+k,-k,-l Rotation: 2 ; direction: (2, 1, 0) ; screw/glide: (0,0,0) -x,-x+y,-z -h-k,k,-l Rotation: 2 ; direction: (0, 1, 0) ; screw/glide: (0,0,0) y,x,-z k,h,-l Rotation: 2 ; direction: (1, 1, 0) ; screw/glide: (0,0,0) -x+y,y,-z -h,h+k,-l Rotation: 2 ; direction: (1, 2, 0) ; screw/glide: (0,0,0) Note that if group H is centered (C,P,I,F), elements corresponding to centering operators are omitted. (This is because internally the calculations are done with the symmetry of the reduced cell) Splitting data in centrics and acentrics Number of centrics : 306 Number of acentrics : 5664 Patterson analyses ------------------ Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.000 0.000 0.239 Distance to origin : 18.971 Height (origin=100) : 7.557 p_value(height) : 4.031e-01 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 4.031e-01. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Systematic absences ------------------- The following table gives information about systematic absences. For each operator, the reflections are split in three classes: Absent : Reflections that are absent for this operator. Non Absent: Reflection of the same type (i.e. (0,0,l)) as above, but they should be present. Complement: All other reflections. For each class, the <I/sigI> is reported, as well as the number of 'violations'. A 'violation' is designated as a reflection for which a I/sigI criterion is not met. The criteria are Absent violation : I/sigI > 3.0 Non Absent violation : I/sigI < 3.0 Complement violation : I/sigI < 3.0 Operators with low associated violations for *both* absent and non absent reflections, are likely to be true screw axis or glide planes. Both the number of violations and their percentages are given. The number of violations within the 'complement' class, can be used as a comparison for the number of violations in the non-absent class. ------------------------------------------------------------------------------------------------------------------------------------------- | Operator | absent under operator | | not absent under operator | | all other reflections | | | | | <I/sigI> (violations) | n absent | <I/sigI> (violations) | n not absent | <I/sigI> (violations) | n compl | Score | ------------------------------------------------------------------------------------------------------------------------------------------- | 6_0 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_1 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_2 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_3 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_4 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_5 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | ------------------------------------------------------------------------------------------------------------------------------------------- Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of absent violations are listed under the '+++' column. The number of present violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ----------------------------------------------------------------------------------- | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 6 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 61 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 65 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 62 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 64 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 63 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | ----------------------------------------------------------------------------------- Wilson ratio and moments Acentric reflections <I^2>/^2 :2.073 (untwinned: 2.000; perfect twin 1.500) <F>^2/<F^2> :0.776 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.750 (untwinned: 0.736; perfect twin 0.541) Centric reflections <I^2>/^2 :3.729 (untwinned: 3.000; perfect twin 2.000) <F>^2/<F^2> :0.580 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :1.089 (untwinned: 0.968; perfect twin 0.736) NZ test (0<=z<1) to detect twinning and possible translational NCS ----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.104 | 0.095 | 0.320 | 0.248 | | 0.2 | 0.194 | 0.181 | 0.438 | 0.345 | | 0.3 | 0.267 | 0.259 | 0.474 | 0.419 | | 0.4 | 0.342 | 0.330 | 0.487 | 0.474 | | 0.5 | 0.402 | 0.394 | 0.542 | 0.520 | | 0.6 | 0.463 | 0.451 | 0.621 | 0.561 | | 0.7 | 0.512 | 0.503 | 0.641 | 0.597 | | 0.8 | 0.564 | 0.551 | 0.683 | 0.629 | | 0.9 | 0.603 | 0.593 | 0.703 | 0.657 | | 1.0 | 0.644 | 0.632 | 0.712 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.014 | | Maximum deviation centric : 0.093 | | | | <NZ(obs)-NZ(twinned)>_acentric : +0.010 | | <NZ(obs)-NZ(twinned)>_centric : +0.044 | ----------------------------------------------- L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.501 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.336 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. --------------------------------------------- Analysing possible twin law : h,-h-k,-l --------------------------------------------- Results of the H-test on acentric data: (Only 50.0% of the strongest twin pairs were used) mean |H| : 0.012 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.000 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.488 Estimation of twin fraction via cum. dist. of H: 0.489 Britton analyses Extrapolation performed on 0.47 < alpha < 0.495 Estimated twin fraction: 0.453 Correlation: 0.9692 R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.015 R_abs_twin calculated data : 0.018 R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.000 R_sq_twin calculated data : 0.000 Perfoming correlation analyses The supplied calculated data are normalized and artificially twinned Subsequently a correlation with the observed data is computed. Results: Correlation : 0.828109216467 Estimated twin fraction : 0.47 Maximum Likelihood twin fraction determination Zwart, Read, Grosse-Kunstleve & Adams, to be published. The estimated twin fraction is equal to 0.478 Exploring higher metric symmetry The point group of data as dictated by the space group is P 6 the point group in the niggli setting is P 6 (c,a,b) The point group of the lattice is P 6 2 2 (c,a,b) A summary of R values for various possible point groups follow. -------------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | -------------------------------------------------------------------------------------------------- | P 6 2 2 (c,a,b) | 0.015 | 0.015 | None | None | 1.508e+04 | <--- | | P 6 (c,a,b) | None | None | 0.015 | 0.015 | 2.595e+04 | | -------------------------------------------------------------------------------------------------- R_used: mean and maximum R value for symmetry operators *used* in this point group R_unused: mean and minimum R value for symmetry operators *not used* in this point group An automated point group suggestion is made on the basis of the BIC (Bayesian information criterion). The likely point group of the data is: P 6 2 2 (c,a,b) Possible space groups in this point groups are: Unit cell: (81.3899, 81.3899, 79.4753, 90, 90, 120) Space group: P 61 2 2 (No. 178) Unit cell: (81.3899, 81.3899, 79.4753, 90, 90, 120) Space group: P 65 2 2 (No. 179) Note that this analysis does not take into account the effects of twinning. If the data are (almost) perfectly twinned, the symmetry will appear to be higher than it actually is. --------------------------------------------------- Merging in *suggested* point group P 6 2 2 (c,a,b) --------------------------------------------------- R-linear = sum(abs(data - mean(data))) / sum(abs(data)) R-square = sum((data - mean(data))**2) / sum(data**2) In these sums single measurements are excluded. Redundancy Mean Mean Min Max Mean R-linear R-square unused: - 9.9896 bin 1: 9.9896 - 5.9876 1 2 1.665 0.0173 0.0023 bin 2: 5.9876 - 4.9363 1 2 1.733 0.0173 0.0009 bin 3: 4.9363 - 4.3717 1 2 1.767 0.0161 0.0013 bin 4: 4.3717 - 4.0001 1 2 1.789 0.0181 0.0013 bin 5: 4.0001 - 3.7294 1 2 1.817 0.0261 0.0041 bin 6: 3.7294 - 3.5197 1 2 1.805 0.0289 0.0027 bin 7: 3.5197 - 3.3504 1 2 1.827 0.0317 0.0033 bin 8: 3.3504 - 3.2096 1 2 1.831 0.0562 0.0108 bin 9: 3.2096 - 3.0898 1 2 1.831 0.0627 0.0119 bin 10: 3.0898 - 2.9861 1 2 1.847 0.0621 0.0095 unused: 2.9861 - Suggesting various space group choices on the basis of systematic absence analyses Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of absent violations are listed under the '+++' column. The number of present violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ----------------------------------------------------------------------------------- | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 6 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 61 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 65 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 62 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 64 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 63 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | ----------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws <I^2>/^2 : 2.073 <F>^2/<F^2> : 0.776 <|E^2-1|> : 0.750 <|L|>, <L^2>: 0.501, 0.336 Multivariate Z score L-test: 1.562 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. Statistics depending on twin laws ------------------------------------------------------------------------------------ | Operator | type | R_abs obs. | R_abs calc. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------------------------ | h,-h-k,-l | M | 0.015 | 0.018 | 0.453 | 0.489 | 0.478 | ------------------------------------------------------------------------------------ Patterson analyses - Largest peak height : 7.557 (corresponding p value : 0.40308) The largest off-origin peak in the Patterson function is 7.56% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. The symmetry of the lattice and intensity however suggests that the input space group is too low. See the relevant sections of the log file for more details on your choice of space groups. As the symmetry is suspected to be incorrect, it is advicable to reconsider data processing. -------------------------------------------------------------------------------

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xtriage to double-check symmetry
by Frank von Delft 17 Sep '09

17 Sep '09

Hi We were trying to decide whether a structure is P65 or P6522: data merges fine in latter, and NCS is perfect, but R/Rfree are significantly worse (32/37-ish vs 23/28 for P65). So I thought I'd listen to xtriage: seemed easy since I have both data and model in P6522, and I ran: phenix.xtriage final.mtz reference.structure.file=final.pdb I'm not sure it's done anything, though - at least, I can't find the table shown on the 4th-last slide of this presentation: http://aca.hwi.buffalo.edu/HotNews/twinning/zwart.pdf Something I said / did not say? Do I *have* to run it in P1? Thanks! phx

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Autobuild at 5A resolution
by Peter Grey 17 Sep '09

17 Sep '09

Dear Phenix users, I am trying to solve a big RNA/protein complex at 5A resolution. Phases come from MR solution with a partial model in Phaser. Thanks to NCS the map after density modification in RESOLVE is of reasonable quality for this resolution and new secondary structures, out side of the model, can be detected. I would like to improve the maps and model with something like a poor man's version of AutoBuild. An Autobuild for very low resolutions that does not include refinement but iteratively carries out density modification and identification of helices/strands outside of the model with phenix.find_helices_strand. Does this sound feasible, Are there already scripts the follow such a scheme ? Many thanks in advance for your advice -- Peter

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error: running phenix.refine
by RAVINDRA D MAKDE 16 Sep '09

16 Sep '09

Hello all, I will greatly appreciate the help for the following: I am getting the error "RuntimeError: min() argument is an empty array" (more details error message given below) while running phenix.refine. I am using PHENIX: Version: 1.3 on Platform: mac-intel-osx osx-10.5.7 My error message is as follows: Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_utils.py", line 379, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.3-final/iotbx/iotbx/mtz/__init__.py", line 424, in as_miller_arrays and flex.min(column_group.sigmas()) > 0):RuntimeError: min() argument is an empty array Thanks in advance, Regards, Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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Problem with modified cysteine CME
by Kendall Nettles 16 Sep '09

16 Sep '09

I am trying to refine a structure with modified cysteines, which refmac recognized as CME just fine. Phenix has CME listed in the mon_lib_list.cif, but the CME.cif file was not in the mon_lib/c/ directory. I added it to the phenix mon_lib/c directory but phenix.refine still complained. I next added the CME.cif file ( copied from ccp4) as a command line input to phenix.refine, and added this to my parameters file: refinement.pdb_interpretation.apply_cif_modification { data_mod = CME residue_selection = chain A and resid 381 residue_selection = chain B and resid 381 residue selection = chain B and resid 530 } Still no luck. Thanks for your help, Kendall -- Kendall W. Nettles, PhD Associate Professor Department of Cancer Biology The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458

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