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reflection file utils : .cif?
by Bryan W. Lepore 03 Sep '09

03 Sep '09

[ phenix 1.4r3 cctbx tag: 2008_12_07_1353 intel-linux-2.6 redhat-e4.7 ] i obtained a recent .cif from the PDB, then run : phenix.reflection_file_converter --mtz=output.mtz test.cif file_name: test.cif file_type: None No reflection data found in input file. .... not sure where to go from here (a clip of the file is below, hope not too much) - i know i can run ccp4:cif2mtz, but are .cif part of phenix.reflection_file_converter? -bryan (sample of test.cif): data_testsf # _diffrn_radiation.id 1 _diffrn_radiation.pdbx_wavelength 1.00600 # _audit.revision_id 1_0 _audit.creation_date 2009-07-07 _audit.update_record 'Initial release' # _symmetry.Int_Tables_number 1 _symmetry.space_group_name_H-M 'P 1' # _cell.length_a 79.6610 _cell.length_b 104.1490 _cell.length_c 154.0250 _cell.angle_alpha 81.9570 _cell.angle_beta 75.9250 _cell.angle_gamma 73.7280 # _reflns.d_resolution_high 2.967 _reflns.d_resolution_low 46.392 _reflns.limit_h_max 26 _reflns.limit_h_min -25 _reflns.limit_k_max 34 _reflns.limit_k_min -34 _reflns.limit_l_max 51 _reflns.limit_l_min 0 _reflns.number_all 93210 _reflns.number_obs 85990 # loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.status _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au 1 1 1 o -25 -16 1 218.4 77.9 1 1 1 o -25 -15 1 250.7 87.9 1 1 1 o -25 -15 2 217.9 78.8 (... etc... here is a free set hkl :) 1 1 1 f -25 -7 3 315.6 89.7 (... etc... until the end :) #END OF REFLECTIONS

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Custom Planar Restraints
by cheung＠lmb.uni-muenchen.de 03 Sep '09

03 Sep '09

Hi all - is it possible to specify custom planar restraints in phenix.refine? I'm refining a 3.8A protein-dna complex and although i've set hydrogen bonding restraints between base pairs, they still become very twisted and buckled after refinement. Alan

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question about autobuild
by crystallogrphy 03 Sep '09

03 Sep '09

Hi, I have used phenix.automr followed by phenix.autobuild to build a 264 residue model against my 2.1A resolution data set. The first run of autobuild gives me about 180 residues built. I have adjusted the model according to the denity. The N-terminal of the model has OK density to add more residues to the model. Can phenix.autobuild has some command to just put more residues to the N-terminal of my current model according to the density, so that the cost of CPU time will be much less than rerun the job completely? Thanks!

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Chain id of water is not reading by coot
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, I have 7 chains in my pdb file. When I am reading the pdb file in COOT, for some reason the chain id(W) of water is not coming in the list. I clicked on 'draw' and then 'go to atom'. I can see all other chains but not W. I created water in PHENIX Is there any wrong in my pdb? HETATM 7562 O HOH W 542 -9.043 -2.133 -12.633 1.00 34.55 W O HETATM 7563 O HOH W 543 -22.004 8.228 -21.695 1.00 34.55 W O HETATM 7564 O HOH W 544 5.926 38.977 -11.538 1.00 34.55 W O HETATM 7565 O HOH W 545 -31.162 5.813 -31.403 1.00 34.55 W O Raja

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Improving picture quality of ED map in PYMOL
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja

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Source for Nightlys Location?
by Andrew Ring 02 Sep '09

02 Sep '09

Is it possible to get a source distribution for the nightlys? If so, where is it located? I can only finding the builds on the nightlys downloads page. For my systems and uses, the --openmp switch on version 1.4-3 has given encouraging results and I would like to investigate with something newer. -- =================================== Andrew Ring System Administrator Kuriyan Laboratory http://jkweb.qb3.berkeley.edu/ Doudna Laboratory http://rna.berkeley.edu/ University of California, Berkeley Office: 542 Stanley Hall Shipping: 176 Stanley Hall, QB3 Berkeley, CA 94720-3220 tel: (510) 643 0166 fax: (510) 643 2352 ====================================

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R-work is too low
by Sam Stampfer 01 Sep '09

01 Sep '09

Hi, I'm refining a 2.88 Angstrom structure and am getting a difference of greater than 6% between the R-work and R-free. The best result (I think) is what I have from minimization alone: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2424, R-free = 0.3174 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2411, R-free = 0.3176 The results from simulated annealing are the following: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2454, R-free = 0.3322 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2403, R-free = 0.3333 I have also done the refinement with ncs but ncs is probably not appropriate for my structure. The final R-free ends up being higher (though the difference between R-free and R-work ends up being 6-7%) My PI (who is on vacation until next week) said that it was a problem if R-work was more than 0.06 lower than R-free. Any recommendations for me? Is it possible to reduce this difference? Is it worth it to rebuild the refined pdb if the R-work is this different from the R-free? My refinement script is: phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \ output.prefix=results/ss46_rebuilt_sa \ strategy=individual_sites+group_adp cif_link.params nag-nag.cif \ twin_law="h,-h-k,-l" \ simulated_annealing=true (the cif_link.params and nag-nag.cif files are made to handle the N-glycosylation sites, I think). Thanks for your help! -Sam

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error TLS refinement
by Marjolein Thunnissen 01 Sep '09

01 Sep '09

I'm trying to finish refining a structure that has been almost refined completely about a year ago with an older version of Phenix.refine. When I start TLS refinement I get the following error message: RuntimeError : mean_weighted() argument is an empty array Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 259, in OnExcept raise event.data RuntimeError: mean_weighted() argument is an empty array I do not get this error when refining without TLS, only when I switch it on. The program advises me to post the error here so... Thanks Marjolein ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)46-22 24584 Associate Professor Fax +46-(0)46-22 24692 Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations for macromolecular crystallography ________________________________________________________________________

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Specifying the number of processors to run phenix with
by Sam Stampfer 31 Aug '09

31 Aug '09

Hi- anyone know how to specify the number of processors to run phenix under in linux? Or how to tell what the default is? I'm running linux (fedora) with 4 processors and can't tell whether phenix is using all of them or not. I do the refinement with .csh files and tried doing "myfile.csh --nproc=4". The file ran but no faster- I can't tell if it is using 4 by default or if that's the incorrect command to specify the use of 4 processors. Thanks for your help! -Sam

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Best first map for RESOLVE after MR
by Peter Grey 31 Aug '09

31 Aug '09

Hello all, I try to solve the structure of a big complex at rather low resolution. I have a molecular replacement solution with a partial model from Phaser. I would like to use RESOLVE for density modification. I ask for your advice regarding the first map that should be the input into RESOLVE. Should it be the 2mFo-DFc map directly from Phaser or would it be better to do rigid body refinement in phenix.refine and use the bulk solvent corrected 2mFo-DFc map ? Many thanks in advance for your suggestions, Peter.

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high resolution bin statistics
by Sebastiano Pasqualato 31 Aug '09

31 Aug '09

Hi there, i just wanted to know how is determined the number of bins for which the statistics of refinement are given in the header of the pdb refined with phenix.refine, and if there's a way to have more than the number of bins that is default output. For example, what if I'd like to have statistics for the 2.6-2.5 bin, here: REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890 thanks a lot in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094

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question about kick map
by crystallogrphy 29 Aug '09

29 Aug '09

Hi, I am trying to use kick map to remove model bias with the following script phenix.refine MR.1_refine_data.mtz MR.1_refine_001_refine_001.pdb output.prefix=refine-090828a simulated_annealing=True simulated_annealing.start_temperature=8000 strategy=individual_sites refine.params However, the program says: Sorry: Unknown file format: refine.params I do not understand why the format of refine.params cannot be read, which has the following contents. Does anyone know why? refinement { electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } }

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reflection file utility and use of modified phases in refinement
by Engin Ozkan 28 Aug '09

28 Aug '09

Hi everybody, I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)? Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one? Thanks, Engin -- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111

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Tracing and refining b-strands at 3.3A resolution
by Gino Cingolani 28 Aug '09

28 Aug '09

Hi Phenix community, I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? 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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Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution
by Gino Cingolani 28 Aug '09

28 Aug '09

Sean, thanks to you and to whoever else responded to my email. Yes, I'd like to get your script. Thanks in advance! 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: Fri, 28 Aug 2009 08:35:08 +0100 >From: Wai-Ching Hon <hon(a)mrc-lmb.cam.ac.uk> >Subject: Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution >To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > >Dear Sean, > >That sounds wonderful. Can I have your scripts too? > >many thanks > >waiching. > >Sean Johnson wrote: >> Gino, >> >> My lab recently refined a 3.4 A structure and dealt with similar >> problems. We found that using secondary structure restraints was the >> only effective way to maintain reasonable geometry during refinement. It >> is kind of a daunting task to input all of the definitions by hand, so >> we wrote a couple python scripts that are integrated with PyMol to write >> the appropriate restraint definition files. All you have to do is click >> on the atoms that you want restrained. You are welcome to the scripts if >> you like. Feel free to contact me if you are interested. >> >> Sean Johnson >> >> >> Gino Cingolani wrote: >> >>> Hi Phenix community, >>> >>> I'm tracing a 3.3A averaged electron density map of >>> a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? >>> >>> 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 >>> >>> >> >> >________________ >hon.vcf (1k bytes) >________________ >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb

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P43212 spacegroup change to C2221?
by Leigh Allen 28 Aug '09

28 Aug '09

Hello Phenix users. I recently solved the structure of my enzyme using SAD to a resolution of 1.9A. The R values were 0.19/0.25 and the space group was P43212 with a unit cell ~80, 80, 220. I then starting collecting datasets cocrystallized with ATP analogs and noticed that a lot of my datasets have a different unit cell when scaled in P43212. It comes out to be ~60, 60, 220 and I can NOT get a solution in Phaser with this data. If I scale it in C2221, then the unit cell is the same (80, 80, 220), but upon refinement, the R factors don't go much below 0.26/0.32. Has anyone ever seen something like this happen? I'm unsure if I should feel like the solution is C2221 since there are space groups of higher symmetry with similar residuals that seem plausible in indexing just the smaller unit cell. Should I keep trying to get a solution out of the data that leads to different unit cell parameters, but has higher symmetry? Xtriage seems to find twinning, but I think it's from NCS since my ASU contains a homodimer. I could also be wrong about this... Thanks in advance for any advice! ******* Leigh Allen Ph.D Candidate McCafferty Lab Duke University Department of Chemistry

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Questions about molecular replacement.
by Yuan Cheng 27 Aug '09

27 Aug '09

Hi, I am working on solving a protein structure using phenix.automr. There is likely four monomers in a ASU based on phenix.xtriage.I am using a search model with 30% identity with my protein. After finding three monomers in a ASU, the LLG is 1740 and R factor is 56%. After finding the fourth monomer, the LLG increased to 2080,but the R factor also increased to 58%. I have several question here: 1) how much should LLG and R factor be if the model from molecular replacement is correct? I guess the answer might not be a exact number. But I am still wondering what should be the correct range. 2) Whether R factor and LLG should always be positively correlated? I used phenix.refine to refine the model with 3 monomers and the model with 4 monomers in a ASU. The Rwork and Rfree are similar for these two models,47% and 53% respectively. I think that one more monomer should either improve or ruin the model.I don't quite understand why one extra monomer doesn't matter too much here. In addition, do you think it is worthy to keep doing model building and refinement in consideration such high R factors. All you suggestions and opinions will be greatly appreciated! Yuan

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Finding correct Se sites with autosol
by YS. Chung 27 Aug '09

27 Aug '09

Dear all, I have a 3 angstrom structure which I am trying to solve with MAD or SAD. The structure was previously solved with molecular replacement but refinement could not continue due to poor phasing at the N-terminal domain of the protein. I have run solve and autosol which are able to find the Se sites. However, Se sites are not anywhere near the methionines when I superimpose the ha.pdb and the pdb file that I obtain from a new run of molecular replacement. The exptl_fobs_phases_freeR_flags.mtz and the overall_best.pdb do not show any connected densities. I have also tried autobuild with the solutions from AutoSol, but the model that it builds in is incorrect. Any suggestions would be appreciated. Thank you, Yu Seon Chung

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Re: [phenixbb] another difficult space group
by Maia Cherney 26 Aug '09

26 Aug '09

Hi Randy, thank you for your help. Today we collected at the CLS two newer crystals of this form. I will process them and see, if they give me better results. For the dataset that I have done mor. rep, here is information from the headers of solutions P6222: LLG 2194 in p32: LLG 6840 C222: LLG=5252 C2: LLG 7942 P62: LLG 4058 Z-scores are very high, too, between 40 and 60. Refinement of any of these solutions gives Rfree around 50-55%, actually, it goes up at every cycle of refinement. Randy, what is the best file to send to you: which space group for the sca or mtz file , which solution? Maia Randy J. Read wrote: > Hi Maia, > > If it's a molecular replacement issue, we might be able to help. I'd > be happy to look at your data. > > All the best, > > Randy > > On Aug 25 2009, Maia Cherney wrote: > >> Thank you Peter for your reply. >> >> I will try the p1 expansion. Thank you for the suggestion. And really >> data look very good, the Rmerge is very low, chi squares are around >> one, looked like a perfect data set to me; >> >> one molecule in AU (in p6222). The model is exactly the same protein >> solved in two other space groups. >> >> And it's not one crystal, all these bipyramids are like this. I can >> send you my p1.sca if you are curious to look at it. >> >> Maia >> >> >> Peter Zwart wrote: >>> Hi Maia, >>> >>> Two points: >>> >>> 1) : >>> >>> Given that fact that you can process the data in p622, you can expand >>> the data to p1: >>> >>> phenix.reflection_file_converter mydata.sca --sca=p1.sca --expand_to_p1 >>> >>> Eventhough this is not the same as having 'real' p1 data, you know >>> that the data merges well in p622, so no harm is done (or at least not >>> a lot). >>> >>> Do you have pseudo translational symmetry by any chance? I wasn't able >>> to find any relation between the two provided unit cells. It is very >>> curious that their volume are equal though. >>> >>> >>> >>> 2): >>> >>> The fact that you cannot solve it might also be due to the fact that >>> your MR model is incorrect for some obscure reason. >>> >>> >>> HTH >>> >>> Peter >>> >>> >>> >>> >>> >>> >>> >>> >>> 2009/8/25 Maia Cherney <chern(a)ualberta.ca>: >>> >>>> Hi everybody, >>>> >>>> I have two types of hexagonal crystals: rods and bipyramids with >>>> dimensions 150x150x83 (rods) and 142x142x93 (bipyramids). Both >>>> types of >>>> crystals give the same spacegroup P6222. However, the rods gave a good >>>> solution and refined to low R factors, whereas the bipyramids give a >>>> solution with high LLG and Z-score, but don't refine at all (R factors >>>> around 50%). The xtriage does not indicate any twinning. Lower >>>> symmetry >>>> spacegroups (trigonal and monoclinic) have the same problem: give >>>> solutions with high scores that would not refine. The resolution is >>>> 2.3A. Unfortunately, the dataset processed in p1 has only 60% >>>> completeness (as it was collected according to p3 strategy). Should I >>>> try to solve in p1 with this low completeness? What can be a problem? >>>> >>>> Maia >>>> >>>> >>>> >>>> Peter Zwart wrote: >>>> >>>>> Good point. >>>>> >>>>> For now the best thing to do is to read the RvsR paper cited in >>>>> the text. I'll add a section to the manual as well. >>>>> >>>>> Ideally of course, xtriage should make its own judgement. Some >>>>> code is >>>>> there, but I took it out as it is not well-tested (and didn't do the >>>>> job) >>>>> >>>>> P >>>>> >>>>> >>>>> 2009/8/25 Pavel Afonine <PAfonine(a)lbl.gov>: >>>>> >>>>> >>>>>> Hi Peter, >>>>>> >>>>>> do you have any guidance to how interpret this table summarized >>>>>> somewhere in the documentation? Otherwise it looks a bit cryptic >>>>>> to me (I tried it while ago, may be it is improved now). >>>>>> Alternatively, it would be nice if Xtriage prints out its own >>>>>> verdict based on that table. >>>>>> >>>>>> Thanks! >>>>>> Pavel. >>>>>> >>>>>> >>>>>> On 8/25/09 10:47 AM, Peter Zwart wrote: >>>>>> >>>>>> >>>>>>> Subsequently, run >>>>>>> >>>>>>> phenix.xtriage p1data.mtz reference.structure.file=MR.1.pdb >>>>>>> >>>>>>> and start interpreting the RvsR tables. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> >>> >>> >>> >>> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > >

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Re: [phenixbb] Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 26 Aug '09

26 Aug '09

Thanks for everyone's help! I got the refinement working in version 1.4-125 and am all set. -Sam On Tue, Aug 25, 2009 at 4:19 PM, Ben Eisenbraun <bene(a)crystal.harvard.edu>wrote: > There's version 1.4-125 in the SBGrid software tree. Did you try it? Is > that version too old? > > You should ask Katya to update her user list. You're not in our database. > > -ben > > On Tue, Aug 25, 2009 at 04:13:44PM -0400, Sam Stampfer wrote: > > I couldn't get the source code to compile- the final message was: "error: > > configuration step incomplete, exiting". Any ideas? > > Thanks, > > -Sam > > > > [A copy of my problem is pasted here]: > > > > I'm running the latest complete version of phenix (version 1.4-147, on > Linux > > 2.6-x86 64). When I run my .csh file I get the following error (with the > 4 > > previous lines included): > > > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) > > [0x446bdd] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4396e4] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4470a9] > > /lib64/libc.so.6 [0x30fca322a0] > > Segmentation fault (Python and libc call stacks above) > > This crash may be due to a problem in any imported > > Python module, including modules which are not part > > of the cctbx project. To disable the traps leading > > to this message, define these environment variables > > (e.g. assign the value 1): > > BOOST_ADAPTBX_FPE_DEFAULT > > BOOST_ADAPTBX_SIGNALS_DEFAULT > > This will NOT solve the problem, just mask it, but > > may allow you to proceed in case it is not critical. > > > > When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run > my > > .csh file, it runs for a slightly longer period of time before ending > with a > > different error: > > > > 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 > > /lib64/libbz2.so.1.0.4 > > 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 > > 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 > > 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 > > 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 > > 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so > > 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort > > > > However, the file ran fine and successfully output an improved .pdb file > > without any BOOST-related problems on my PI's Mac- she is running version > 95 > > of Phenix (which I was unable to obtain for linux- is it available > > somewhere?) > > > > Can you help me with this? > > > > Thanks! > > > > -Sam > > > > > > On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve > > <rwgk(a)cci.lbl.gov>wrote: > > > > > Could you try with a source installation? > > > > > > > > > > https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show… > > > > > > I recommend you rm -rf the binary installation before ./install from > > > sources. > > > Add > > > --nproc=N > > > to the ./install command to use all N cpus in your machine for the > > > installation. > > > > > > Let me know if the problem persists. > > > > > > Ralf > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > -- > | Ben Eisenbraun | Tools Sysadmin | > | Structural Biology Grid | http://sbgrid.org | > | Harvard Medical School | http://hms.harvard.edu | > >

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Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 25 Aug '09

25 Aug '09

Hi, I'm running the latest complete version of phenix (version 1.4-147, on Linux 2.6-x86 64). When I run my .csh file I get the following error (with the 4 previous lines included): /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) [0x446bdd] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4396e4] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4470a9] /lib64/libc.so.6 [0x30fca322a0] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my .csh file, it runs for a slightly longer period of time before ending with a different error: 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 /lib64/libbz2.so.1.0.4 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort However, the file ran fine and successfully output an improved .pdb file without any BOOST-related problems on my PI's Mac- she is running version 95 of Phenix (which I was unable to obtain for linux- is it available somewhere?) Can you help me with this? Thanks! -Sam

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ruthenium parameters
by Terry Lang 25 Aug '09

25 Aug '09

Hey Everyone, I am working on an xray structure that contains a ruthenium. I have been able to use elbow to create a cif file that phenix can read and refine without throwing error messages. However, there is a large amount of positive electron density after the refinement. I am looking into modeling coordinate waters, but I first wanted to check that the ruthenium is being read correctly by phenix. How do I figure out if it is properly recognized (eg correct scattering factors, bond and angle restraints, etc)? Thanks, Terry -- P. Therese Lang Postdoctoral Scholar Alber Lab, UC Berkeley

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phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 24 Aug '09

24 Aug '09

Hi folks: About a year ago I refined a 1.6 Å RNA structure with phenix.refine 1.3b-rc6 and then got distracted. I picked it up today and essentially repeated the last round of refinement with 1.4-57 (and also 1.4-159). The maps are subtly different, but consistently slightly worse with 1.4. Here are two examples: http://sage.ucsc.edu/~wgscott/mystuff/old_vs_new.pdf In the second example, this would lead to deletion of one of the octahedrally coordinated waters on a known Mg++ ion. 2OEU is similar, except 2.0 Å resolution, and it has Mn2+ instead of Mg ++. A similar thing happens with the corresponding water in that structure. Has the weighting for the bulk solvent mask or something like that been increased? Thanks. Bill Scott

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difference in B factor for NCS groups
by James Whittle 21 Aug '09

21 Aug '09

Dear all, I'm working with a structure were one NCS copy has significantly high B-factors than the other. That one copy makes few crystal contacts to stabilize it. Is there a recommended way to adjust the refinement to reflect this ... using TLS? Decreasing b_factor_weight? Is there a way refine a group_b to be added to the b-factor of each atom in that chain? --James

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Error in running Autosol....
by S. Karthikeyan 20 Aug '09

20 Aug '09

Dear All, I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation. I am trying to solve a structure of Se-Met through phenix.autosol_gui. Once the programs starts it goes to several stages including converting from mtz to sca, xtriage and so on. Finally it gives an error message as follows: ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) ******************************************************************************** I found the LAST.LOG file is empty. I am trying to find out what could be problem? Any suggestions or help is much appreciated! Thanking you S.Karthikeyan

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