- phenixbb - phenix-online.org

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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