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Re: [phenixbb] mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by Thomas C. Terwilliger 08 Jun '11

08 Jun '11

Hi Jorge, In your version of phenix yes, you need a special format for the alignment files. I just changed it to allow a simple alignment file: >target sequence-of-target >template sequence-of-template which is also used by sculptor. This is available in a current nightly build. You can then just paste the alignment from hhpred into such a file. I hope that helps! -Tom T >>> Thanks, Tom. >> Yes, phenix.mr_model_preparation fails just like phenix.mr_rosetta: >> >> " >> Traceback (most recent call last): >> File >> "/usr/local/phenix-1.7.1-743/phaser/phaser/command_line/mr_model_preparation.py", >> line 9, in <mod ule> >> mr_model_preparation.run( args = sys.argv[1:], out = sys.stdout ) >> File >> "/usr/local/phenix-1.7.1-743/phaser/phaser/mr_model_preparation.py", >> line 255, in run >> proxy = proxy.DbfetchHTTP( database = "pdb", format = "pdb" ) >> File "/usr/local/phenix-1.7.1-743/phaser/phaser/proxy.py", line 108, in >> __init__ >> raise RuntimeError, "Cannot contact %s" % str( self ) >> RuntimeError: Cannot contact EBI DbFetch service >> " >> >> I think I will have to go to phenix sculptor. This seems to require >> the alignment in ".aln (CLUSTAL format), .pir (PIR-format) and .ali >> (relaxed PIR-like format)" maybe I could prefer to keep the hhr >> alignment but I will have to check if there is an easy way to translate >> one format into the other. Apart from this, phenix.mr_rosetta, seems to >> require the alignment "MODELLER-style". >> Therefore, to keep the alignment as output by hhr (is this wise? >> Does this use multialignment and maight this be better that pairwise >> alignment?) I have to translate it to either aln/pir/ali (for phenix >> sculptor) and then to MODELLER-style for phenix.mr-rosetta. >> A suggestion to make this more straight forward? >> >> J. >> >>> Hi Jorje, >>> >>> Yes, you can prepare your model separately from mr_rosetta. You can do >>> this (for example) with: >>> >>> phenix.mr_model_preparation 3800765_mod_ed.hhr >>> >>> If that fails with the same download problem, you can create an >>> alignment >>> file and use phenix.sculptor to edit your model. >>> >>> Then as you suggest, you can use your edited model directly as a >>> "search_model" and skip the .hhr files entirely. >>> >>> Let me know if that doesn't do it! >>> All the best, >>> Tom T >>> >>>>> Dear all, >>>>> >>>>> >>>>> I would like to use mr_rosetta with homolgy search. I followed >>>>> the >>>>> instructions at >>>>> http://www.phenix-online.org/documentation/mr_rosetta.htm , generated >>>>> the hhr and the fragment files, but at submitting the job I receive >>>>> the >>>>> message: >>>>> >>>>> ******************* ERROR ENDING *************** >>>>> Cannot contact EBI DbFetch service >>>>> >>>>> ******************* ERROR ENDING *************** >>>>> >>>>> after both loading the file 3800765_mod_ed.hhr and generating the log >>>>> file mr_model_preparation.log. >>>>> >>>>> Concerning this problem, I saw >>>>> http://www.phenix-online.org/documentation/faqs.htm#anch8 . But I am >>>>> not >>>>> behind a proxy and even disabling completely the firewall, the message >>>>> still appears. >>>>> Maybe this is more linux related, I use openSuSE 11.4. >>>>> One workaround would be that I write a script to wget the pdb >>>>> files >>>>> (listed in .hhr) and select the due chains, putting these in a certain >>>>> location and indicating in my script where they are. But I am a kind >>>>> of >>>>> confused, might >>>>> >>>>> search_models= >>>>> >>>>> do this. I am not sure I could use a hhr file together with it. >>>>> Anyway, >>>>> this might be a desirable solution for me yet I use to run my stuff in >>>>> a >>>>> laptop which goes around by. >>>>> >>>>> Thanks, >>>>> >>>>> Jorge >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >>

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XDS format
by Jianghai Zhu 08 Jun '11

08 Jun '11

Hi, In the manual of version 1.7.1, I found out that only phenix.hyss can read XDS_ASCII files with merged data. Do other phenix tools recognized XDS_ASCII files? If not, I would like to request this feature. For example, let phenix.autosol read XDS_ASCII file with merged or unmerged data. Thanks. -- Jianghai

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Re: [phenixbb] mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by iulek＠interponta.com.br 07 Jun '11

07 Jun '11

Thanks, Tom. Yes, phenix.mr_model_preparation fails just like phenix.mr_rosetta: " Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phaser/phaser/command_line/mr_model_preparation.py", line 9, in <mod ule> mr_model_preparation.run( args = sys.argv[1:], out = sys.stdout ) File "/usr/local/phenix-1.7.1-743/phaser/phaser/mr_model_preparation.py", line 255, in run proxy = proxy.DbfetchHTTP( database = "pdb", format = "pdb" ) File "/usr/local/phenix-1.7.1-743/phaser/phaser/proxy.py", line 108, in __init__ raise RuntimeError, "Cannot contact %s" % str( self ) RuntimeError: Cannot contact EBI DbFetch service " I think I will have to go to phenix sculptor. This seems to require the alignment in ".aln (CLUSTAL format), .pir (PIR-format) and .ali (relaxed PIR-like format)" maybe I could prefer to keep the hhr alignment but I will have to check if there is an easy way to translate one format into the other. Apart from this, phenix.mr_rosetta, seems to require the alignment "MODELLER-style". Therefore, to keep the alignment as output by hhr (is this wise? Does this use multialignment and maight this be better that pairwise alignment?) I have to translate it to either aln/pir/ali (for phenix sculptor) and then to MODELLER-style for phenix.mr-rosetta. A suggestion to make this more straight forward? J. > Hi Jorje, > > Yes, you can prepare your model separately from mr_rosetta. You can do > this (for example) with: > > phenix.mr_model_preparation 3800765_mod_ed.hhr > > If that fails with the same download problem, you can create an alignment > file and use phenix.sculptor to edit your model. > > Then as you suggest, you can use your edited model directly as a > "search_model" and skip the .hhr files entirely. > > Let me know if that doesn't do it! > All the best, > Tom T > >>> Dear all, >>> >>> >>> I would like to use mr_rosetta with homolgy search. I followed the >>> instructions at >>> http://www.phenix-online.org/documentation/mr_rosetta.htm , generated >>> the hhr and the fragment files, but at submitting the job I receive the >>> message: >>> >>> ******************* ERROR ENDING *************** >>> Cannot contact EBI DbFetch service >>> >>> ******************* ERROR ENDING *************** >>> >>> after both loading the file 3800765_mod_ed.hhr and generating the log >>> file mr_model_preparation.log. >>> >>> Concerning this problem, I saw >>> http://www.phenix-online.org/documentation/faqs.htm#anch8 . But I am not >>> behind a proxy and even disabling completely the firewall, the message >>> still appears. >>> Maybe this is more linux related, I use openSuSE 11.4. >>> One workaround would be that I write a script to wget the pdb files >>> (listed in .hhr) and select the due chains, putting these in a certain >>> location and indicating in my script where they are. But I am a kind of >>> confused, might >>> >>> search_models= >>> >>> do this. I am not sure I could use a hhr file together with it. Anyway, >>> this might be a desirable solution for me yet I use to run my stuff in a >>> laptop which goes around by. >>> >>> Thanks, >>> >>> Jorge >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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polygon Error.
by Yuri 07 Jun '11

07 Jun '11

Hello everyone, Keep getting an error when I try to run polygon to validate my model. Here is what i get: RuntimeError : lbfgs error: Line search failed: The step is at the lower bound stpmin(). Traceback: File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/libtbx/thread_utils.py", line 223, in run return_value = self._target(self._args, self._kwargs, self._c) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__ result = self.target() File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/phenix/phenix/validation/analyze_all.py", line 358, in __call__ result = validation_result(params, tmp_dir) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/phenix/phenix/validation/analyze_all.py", line 139, in __init__ return_fmodel_and_pdb=True) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/model_vs_data.py", line 806, in run mvd_obj.collect(model_vs_data = show_model_vs_data(fmodel)) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/model_vs_data.py", line 556, in show_model_vs_data sigmaa_plot = fmodel.sigmaa().show_short(silent=True) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 1464, in sigmaa use_sampling_sum_weights = p.use_sampling_sum_weights) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/scaling/sigmaa_estimation.py", line 191, in __init__ w_obs=w_obs) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/math/chebyshev_lsq_fit.py", line 72, in __init__ self.minimizer = lbfgs.run(target_evaluator=self) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/lbfgs/__init__.py", line 258, in run log) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/lbfgs/__init__.py", line 143, in run_c_plus_plus if (minimizer.run(x, f, g)): continue Thank you -- Yuri Pompeu

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mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by iulek＠interponta.com.br 07 Jun '11

07 Jun '11

Dear all, I would like to use mr_rosetta with homolgy search. I followed the instructions at http://www.phenix-online.org/documentation/mr_rosetta.htm , generated the hhr and the fragment files, but at submitting the job I receive the message: ******************* ERROR ENDING *************** Cannot contact EBI DbFetch service ******************* ERROR ENDING *************** after both loading the file 3800765_mod_ed.hhr and generating the log file mr_model_preparation.log. Concerning this problem, I saw http://www.phenix-online.org/documentation/faqs.htm#anch8 . But I am not behind a proxy and even disabling completely the firewall, the message still appears. Maybe this is more linux related, I use openSuSE 11.4. One workaround would be that I write a script to wget the pdb files (listed in .hhr) and select the due chains, putting these in a certain location and indicating in my script where they are. But I am a kind of confused, might search_models= do this. I am not sure I could use a hhr file together with it. Anyway, this might be a desirable solution for me yet I use to run my stuff in a laptop which goes around by. Thanks, Jorge

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a double conformation residue included in metal coordination file
by Yamei Yu 07 Jun '11

07 Jun '11

HI all, In my structure, there is a double conformation residue and on conformation is coordinated to a metal. I use phenix.metal_coordination to generate a elbow.edits file. In such file the restraint listed as: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain B and resname MG and resseq 2001 atom_selection_2 = name OD2 and altid A and chain B and resname ASP and resseq 271 distance_ideal = 2.070000 sigma = 0.100 } } But when I use this file for refinement, I got an error message: Sorry: No atom selected: "name OD2 and altid A and chain B and resname ASP and resseq 271" I also check my PDB file: ATOM 6100 N AASP B 271 -19.420 19.064 51.907 0.50115.36 N ANISOU 6100 N AASP B 271 14002 14643 15186 -598 738 -1235 N ATOM 6101 CA AASP B 271 -18.016 18.977 51.528 0.50127.08 C ANISOU 6101 CA AASP B 271 15508 16123 16656 -585 725 -1202 C ATOM 6102 C AASP B 271 -17.194 19.859 52.460 0.50105.81 C ANISOU 6102 C AASP B 271 12832 13418 13952 -583 730 -1182 C ATOM 6103 O AASP B 271 -17.750 20.593 53.277 0.50 67.89 O ANISOU 6103 O AASP B 271 8027 8614 9153 -586 738 -1193 O ATOM 6104 CB AASP B 271 -17.818 19.429 50.080 0.50154.71 C ANISOU 6104 CB AASP B 271 18986 19641 20157 -560 689 -1204 C ATOM 6105 CG AASP B 271 -18.871 18.868 49.141 0.50167.83 C ANISOU 6105 CG AASP B 271 20622 21317 21830 -559 682 -1230 C ATOM 6106 OD1AASP B 271 -18.804 17.661 48.823 0.50157.05 O ANISOU 6106 OD1AASP B 271 19265 19945 20462 -568 691 -1224 O ATOM 6107 OD2AASP B 271 -19.758 19.638 48.708 0.50156.92 O ANISOU 6107 OD2AASP B 271 19211 19952 20460 -550 666 -1256 O ATOM 6108 N BASP B 271 -19.303 18.972 52.212 0.50115.36 N ANISOU 6108 N BASP B 271 14002 14643 15186 -598 738 -1235 N ATOM 6109 CA BASP B 271 -17.822 18.681 52.128 0.50127.08 C ANISOU 6109 CA BASP B 271 15508 16123 16656 -585 725 -1202 C ATOM 6110 C BASP B 271 -17.006 19.773 52.851 0.50105.81 C ANISOU 6110 C BASP B 271 12832 13418 13952 -583 730 -1182 C ATOM 6111 O BASP B 271 -17.610 20.704 53.419 0.50 67.89 O ANISOU 6111 O BASP B 271 8027 8614 9153 -586 738 -1193 O ATOM 6112 CB BASP B 271 -17.514 18.729 50.592 0.50154.71 C ANISOU 6112 CB BASP B 271 18986 19641 20157 -560 689 -1204 C ATOM 6113 CG BASP B 271 -16.455 17.692 50.152 0.50167.83 C ANISOU 6113 CG BASP B 271 20622 21317 21830 -559 682 -1230 C ATOM 6114 OD1BASP B 271 -16.846 16.720 49.601 0.50157.05 O ANISOU 6114 OD1BASP B 271 19265 19945 20462 -568 691 -1224 O ATOM 6115 OD2BASP B 271 -15.310 17.950 50.520 0.50156.92 O ANISOU 6115 OD2BASP B 271 19211 19952 20460 -550 666 -1256 O Is there something wrong? Thank you very much! yamei yu

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problem with hhr files in phenix_mr.rosetta
by Miguel Ortiz Lombardia 07 Jun '11

07 Jun '11

Dear phenix developers, Trying to run a test job with phenix_mr.rosetta on a Mac (10.6.7) using a command line such as (phenix is the dev-764 version): phenix.mr_rosetta seq_file=this.seq data=P41212.mtz hhr_files=ed593l.hhr hhr_files=ed593g.hhr fragment_files=frag3.gz fragment_files=frag9.gz rescore_mr.relax=False rosetta_models=20 ncs_copies=3 space_group=p41212 use_all_plausible_sg=False nproc=100 group_run_command=qsub I get this kind of error: ******************* ERROR ENDING *************** Uninterpretable: 'Q ss_pred --------------------------------------------------------------------------------\nQ ed593 390 -------------------------------------------------------------------------------- 389 (593)\nQ Consensus 390 -------------------------------------------------------------------------------- 389 (593)\n\nT Consensus 623 ~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 702 (1010)\nT 2xgj_A 623 GKDNYGWGAVVDFAKRINKRNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLD 702 (1010)\nT ss_dssp TTEEEEEEEEEEEEECCCSSCTTCCCCTTTTEEEEEEEEEEETTSCGGGCCTTCCCCCTTCCBCCTTCCEEEEEEEECGG\nT ss_pred CccccceeEEEeeccccccCCCCceeeccccceeeeeecccccCCcccccccccccCccccCcccccccceeEEEEeehh\n\n\nQ ss_pred --------------------------------------------------------------------------------\nQ ed593 390 -------------------------------------------------------------------------------- 389 (593)\nQ Consensus 390 -------------------------------------------------------------------------------- 389 (593)\n\nT Consensus 703 ~i~~i~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~ 782 (1010)\nT 2xgj_A 703 SIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMR 782 (1010)\nT ss_dssp GEEEEEEEECCCCSSTTCSSSHHHHHHHHHHHHHHSSSCCCBCCTTTTSCCCCHHHHHHHHHHHHHHHHHTTSHHHHSSS\nT ss_pred hhhcccceEEecCccccChHHHHHHHHHHHHHHHhCccCCcccCchhhccCCcHHHHHHHHHHHHHHHHHhcCccccCcC' ******************* ERROR ENDING *************** I thought that could be due to different line endings in Macs vs. UNIX, so I transformed the hhr files with (unix2mac is unix2dos 5.3 (2011-04-26)from Fink) unix2mac ed593l.hhr unix2mac ed593g.hhr But then the same input line results in: (...) Loading PDB and alignment files from /a/people/miguel/Lab/Rosetta/MR_ROSETTA_6/WORK_1/ed593l_1/ed593l_ed.hhr Log file for mr_model_preparation is: /a/people/miguel/Lab/Rosetta/MR_ROSETTA_6/WORK_1/ed593l_1/mr_model_preparation.log ******************* ERROR ENDING *************** Incorrect file format ******************* ERROR ENDING *************** Any other ideas? Thank you! -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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meaning of nproc in mr_rosetta
by Miguel Ortiz Lombardía 07 Jun '11

07 Jun '11

Dear Phenix developers, Could you elaborate on the meaning of "nproc" in phenix.mr_rosetta? I tried unsuccessfully to find out in the docs. Please, let me know if I missed something. I sent out a master job to an SGE queue engine, having set nproc=64. At this moment I find 168 jobs submitted and running and the total number of processors in use seems to be around 120. Better understanding of the meaning of nproc would help with the allocation of resources. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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The SASTBX webserver
by Peter Zwart 03 Jun '11

03 Jun '11

Dear All, I would like to advertise our online server featuring some basic SAXS analyses tools. The website http://sastbx.als.lbl.gov/cgi-bin/index.html has functionality for 1. Model intensity calculation (using a Spherical Harmonic Expansion; sastbx.she ) 2. Shape determination (or better: Shape Recovery; sastbx.shapeup) 3. Model alignment (sastbx.zalign) The applications we have developed are build using the SASTBX, an extension of the CCTBX (http://cctbx.sf.net) framework, dedicated to the analyses of SAXS data. The model intensity calculation engine uses an approach similar to CRYSOL and (in our hands) provides model SAXS data of a similar quality as FOXS and CRYSOL. The shape recovery procedure (shapeup) provides an estimate of the shape typically within 1 minute without the need for preprocessing the data (i.e. just feed it your background subtracted SAXS curve and nothing more). You can provide a known model as well for comparison. Some example shape recovery results can be found here: http://sastbx.als.lbl.gov/grant/shapeup/summary.html The examples were prepared utilizing data provided by Edward Snell and coworkers (Grant, T. D., Luft, J. R., Wolfley, J. R., Tsuruta, H., Martel, A., Montelione, G. T. and Snell, E. H. (2011), Small angle X-ray scattering as a complementary tool for high-throughput structural studies. Biopolymers, 95: 517–530). Feel free to contact me or Haiguang Liu (HGLiu(a)lbl.gov) if you encounter any problems or have questions. Regards, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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omit map
by Desi Mail 03 Jun '11

03 Jun '11

Hi everybody, I would like to calculate the omit map around the ligand. I followed the documentation http://www.phenix-online.org/documentation/autobuild.htm#anch159 But the 2Fo density around the ligand is very poor. Any help is appreciated. Thanks Mary Make a SA-omit map around atoms in target.pdb phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit Coefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz).

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