- phenixbb - phenix-online.org

the different between 2mFo-DFc and mFo-DFc map
by 丁玮 30 Jun '09

30 Jun '09

hi,everybody, By phenix.refine outputde two likelihood-weighted maps: 2mFo-DFc and mFo-DFc.When they were displayed in coot, There is a vast difference between them, why? Thanks dream830106 　　　　　　　　dingding830106(a)sina.com 　　　　　　　　　　2009-06-30

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Autobuild requires more then 24 hrs to run on 32 cpu?
by Tatyana Sysoeva 30 Jun '09

30 Jun '09

Hello! I am trying to use Autobuild wizard and it seems that it takes longer time that I expected. That's why I have next questions: 1. What is "usual" time range estimate for Autobuild run with default parameters if my model has 7 chains with 284 aa in each? (if I'm running Autobuild on a single machine it does not finish in 3 days or on cluster with usage of 32 processors - in 24 hours) 2. Do I use phenix comman correctly for using several machines at once? I used /phenix-1.4-89, command line *phenix.autobuild data=e239a.hkl seq_file=seq.dat model=model.pdb nproc=32* In 24 hrs, which is my limit on cluster time, I get next things - AutoBuild_run_1_1_/AutoBuild_run_1_1.log ends with *Setting up to build 5 models to be combined into final model #1 NOTE: input model will be rebuilt in place: nothing will be added or deleted. Building 5 models ... Running up to 32 jobs in parallel... Splitting work into 5 jobs and running 32 at a time with csh in /home2/tas354/phenix_runs/20090610/1/AutoBuild_run_1_/TEMP0 Starting job 1... Starting job 2... Starting job 3... Starting job 4... Starting job 5...* AutoBuild_run_1_1_/TEMP0/AutoBuild_run_1_N.log ends with *Copying refined_pdb_in.pdb to composite_model.pdb in AutoBuild_run_1_/TEMP0 Beginning merge with current best model: refined_pdb_in.pdb Merging models: composite_model.pdb refine_1.pdb Refining model: Build_composite_3.pdb Model: AutoBuild_run_1_/TEMP0/Build_composite_refined_3.pdb R/Rfree=0.23/0.25 Rebuilding side chains from Build_composite_refined_3.pdb* or with error * TRIED resolve_extra_huge ...but not OK ******************************************************************************** Failed to carry out AutoBuild_build_cycle: ******************************************************************************** * Should I change parameters of the Autobuild which will dramatically reduce time for computations or should I ask for extension of my time for letting the programs to run as it is? I would give more details if it is needed I just could not think of some other right now. And I would appreciate any advices and suggestions! Thank you Tanya

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phenix.refine simulated annealing modes
by Alejandro Buschiazzo 29 Jun '09

29 Jun '09

Dear Phenix users, I can't find information on the precise meaning of the different modes to perform SA during refinement; some choices are self-explanatory (such as "every_macro_cycle" or "second_and_before_last"), but what about "once" or "first_half"? (in my particular case, I want to perform only one simulated annealing routine on the second macro_cycle: can I use "once"? but, where should I define at which cycle to perform it?) Thank you for your help, Best, -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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questoin about AutoBuild
by crystallogrphy 27 Jun '09

27 Jun '09

Deal All, After I tried 9 runs of AutoSol from my MAD data by changing parameters (resolution, heavy atom numbers), I got 9 results, named as: AutoSol_run_1_ to AutoSol_run_9_. I found #9 and #7 have the lowest Rfree, so I want to pick the model from these two runs. However, when I use "phenix.autobuild after_autosol", the resulting AutoBuild files tell me that the program picked the result from #5 of AutoSol, not the lastest #9. Does anyone know how can I specify the exact number of AutoSol to run autobuild? I also tried this command "phenix.autobuild data=resolve_3.mtz model=overall_best.pdb seq_file=zntb-sd.seq"under the directory of AutoSol_run_9_, but failed with the following word: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_overall_best_edited.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... See AutoBuild_run_2_/LAST.LOG for more information Please resolve the R-free flags mismatch. ******************************************************************************** Does anyone know where is wrong? Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

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"phenix.fobs_minus_fobs_map" new tool in PHENIX
by Pavel Afonine 27 Jun '09

27 Jun '09

Hi Everyone, for all of you who asked about computing Fo-Fo map in PHENIX: I added a new command line tool called "phenix.fobs_minus_fobs_map". For usage details just type phenix.fobs_minus_fobs_map and hit Enter, and it will print a couple of examples. Any feedback will be very appreciated. This is available in development version of PHENIX starting from 1.4-51: goto: http://www.phenix-online.org/download/ then click "Latest installers" under "Nightly builds (version 1.4-4 and above)" section. Pavel.

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Refining partially occupied DNA on top of itself
by bschmidt＠berkeley.edu 26 Jun '09

26 Jun '09

Hello, I am having difficulty using Phenix to build and refine a DNA duplex. The issue is that my asymmetric unit consists of one protein monomer bound to DNA, but the protein is a dimer and the DNA is not palindromic, so each monomer is bound to a different sequence of DNA. As such, the density for the two different DNA half-sites is averaged out in the asymmetric unit. I have tried to place two duplexes directly on top of one another, each with 0.5 occupancy, and then refine. But I have noticed two problems. The first is that when xyz refinement is off, and I look at the output files, the density for DNA is awfully green, as if there were only *one* helix with 0.5 occupancy there. The other problem I noticed is that when I turn xyz refinement on, and look at the output files, one of the two half-sites gets moved several angtroms, so that it is in a region that generally has no density. I expect that, if done properly, the backbone of both half-site DNAs ought not to move. Any advice would be greatly appreciated. Thanks, Bryan Schmidt

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multi-xtal averaging vs twinning
by Frank von Delft 26 Jun '09

26 Jun '09

Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement. 1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish) 2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too. 3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A). So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not. Or how *would* one approach this? Cheers Frank

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Fix for autobuild/ligandfit problem with long $PATH
by Tom Terwilliger 25 Jun '09

25 Jun '09

Hi Phenix users, Several of you have had trouble with phenix.autobuild (or phenix.ligandfit) failing if you had a very long $PATH. The problem seems to be that if your $PATH is very long, then adding more to it and re-setting it can lead to a string that is too long (on some systems). Starting with PHENIX version 1.4-100 (today's version) you can add the keyword remove_path_word_list=" cns xiaroot ccp4 phaser" to shorten your $PATH. This keyword will selectively remove all paths from $PATH that include any of the words you specify, and that do not include the word "phenix", when running that phenix job. The log file will list what paths were removed. To figure out what paths to remove, type echo $PATH and choose the ones that identify other programs that are not part of phenix. I hope that will do it! Please let me know if this doesn't solve the problems. All the best, Tom T 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

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How to apply geometry regularization to selected residues in phenix.pdbtools
by Oliv Eidam 25 Jun '09

25 Jun '09

Hi, I was wondering if the geometry regularization in phenix.pdbtools can be applied to selected residues only. Something like: > phenix.pdbtools my.pdb selection="resname xyz" --geometry-regularization Many thanks in advance, Oliv -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eidamo(a)blur.compbio.ucsf.edu

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pseudo translational symmetry
by youssef ben ammar 23 Jun '09

23 Jun '09

Hi all, I recently solved the structure of a protein containing 395aa using phenix autosol. After autoBuild I got about 65% of the sequence docked with 2 monomers in the ASU. After several refinement cycles the map has been improved and I build manually the remaining amino acids. But the problem is that R and Rfree didn't decrease below 0.28 and 0.33 respectively. I tried with NCS restraints, TLS but without success. When I revised phenix autosol logs carefully, I found that in xtriage the analyses of the Patterson function reveals a significant off-origin peak that is 41.59 % of the origin peak, indicating pseudo translational symmetry and no twin laws were found. The space group is P212121 (36.898, 59.45, 393.908, 90, 90, 90). The basic statistics suggested 1 copy in the ASU (but the solution gave 2 copies per ASU !!!). The same analysis done by ccp4i gave the same solvent content and math. coef. in p21212 but with 2 copies per ASU. In xtriage I found this suggestion: If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group P 21 21 2 (b-1/4,2*c,a) operator x, y+1/2, z unit cell of reference setting (393.91, 36.90, 29.73, 90.00, 90.00, 90.00) I am really stucked with the refinement and don't know how to deal with this pseudo translation. Any help or suggestions are welcome. Thank you. Youssef

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