- phenixbb - phenix-online.org

Polygon error
by Yuri 08 Jun '11

08 Jun '11

Great Pavel, thanks -- Yuri Pompeu

1 0

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 >>> >> >>

1 0

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

7 10

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 >

1 0

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

2 2

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

2 1

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

2 1

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.

3 3

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.

2 3

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 -----------------------------------------------------------------

1 0

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).

6 8

Diamond Light Source phase III beamline proposal - call for support.
by Johan Turkenburg 03 Jun '11

03 Jun '11

Many of you will already have seen the request for Expressions of Interest for the Diamond phase III proposal for "A versatile microfocus beamline with an in-situ side station for macromolecular crystallography at DIAMOND". As one of the co-proposers I would like to urge you to support this proposal and write a letter to this effect. We need as many as possible! Details of the proposal can be found here, with a link where your letter of support can be uploaded: http://www.diamond.ac.uk/Home/Beamlines/PhaseIII/ExpressionsofInterest.html You may already have been contacted by other colleagues in the MX community but this is of high importance to the structural community as a whole, and we especially invite our international colleagues to provide support for this initiative. To help us collate these EOI's and comment on any additional feedback you may have, we would ask you to do this by June 8th. Johan Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory University of York Phone (+) 44 1904 328251 York YO10 5DD UK Fax (+) 44 1904 328266

1 0

elbow question
by wtempel 03 Jun '11

03 Jun '11

Dear colleagues, am I alone in thinking that in my example phenix.elbow gave me more than what I was asking for, specifically atom H11 attached to sulfur? Is it added by elbow, or does it originate from the "--chem=tpp" input? Best regards, Wolfram Tempel command line: phenix.elbow --chem=tpp --mogul phenix version: 1.7.1-743

3 4

GUI for phenix_mr.rosetta
by riya doreen 02 Jun '11

02 Jun '11

Dear phenix developers, Is it possible to run phenix_mr.rosetta from the GUI ? Thanks

2 1

Re: [phenixbb] rosetta_mr autobuild failure - typo fixed
by Thomas C. Terwilliger 02 Jun '11

02 Jun '11

Hi again Joe, Typo below (csh vs bash) fixed in this version of the message. -Tom Hi Joe, I'm sorry for the problems in running mr_rosetta! Getting the set up to work is appearing to be a bit of a challenge, particularly on a mac. So the first problem is this: "dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found" In the cases that have come up so far, there have been two problems. Here are the solutions to those two problems: 1. The installation of Rosetta cannot be moved after it is compiled. This is because the path to the libraries (as in the error message above) is compiled into Rosetta. So...if you moved this installation around at all, try remaking the installation and keeping it in its original location. 2. In some cases the path to the libraries can be conflicting between PHENIX and some other definition on your system. In this case you can try the following shell command (before running phenix.mr_rosetta): with csh: setenv PHENIX_TRUST_OTHER_ENV 1 or with bash or sh: export PHENIX_TRUST_OTHER_ENV=1 Hopefully...one of those will fix this problem. Now the second problem...I am not sure what the actual error is in this one. The error message you got is not helpful as you say because it refers to a file path on the machine where I created the test. That path does not actually have to exist however (I just ran the test on another machine that is not connected to that directory and it runs fine). This means there is some other problem that is the real one. (I will get rid of this error message so this won't happen in the future). Can you try this: 1. reproduce the problem: phenix_regression.wizards.test_command_line_rosetta_quick_tests \ test_autobuild 2. have a look at the log files: cat run.log # if not empty, may give a big clue more test_autobuild_current.log # look at end of this file for clues 3. the test_autobuild_current.log log file may refer to a sub-process where the actual problem occurs: Log file for autobuilding will be: /Users/terwill/unix/misc/junk/test_autobuild/WORK_1/autobuild.log in this case that autobuild log file, and files in WORK_1/AutoBuild_run_1_/TEMP0 may give additional clues. Let me know what this shows! All the best, Tom T >> >> Hi all, >> >> I wanted to use the rebuilding feature of Rosetta to help improve the R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8 >> >> installation was succesful, so after editing my .profile to include export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests: >> >> 1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up >> >> 2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta >> >> 3. phenix_regression.wizards.test_command_line_rosetta_quick_tests >> >> While the first was successful (ALL COMMAND_LINE TEST OK), the second reported the following error: >> >> Error: test_command_line_rosetta failed >> >> Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported: >> >> coords1.ali >> coords1.pdb >> fobs.mtz >> mr_rosetta_quick.eff >> perfect.mtz >> seq.dat >> test3.gz >> test9.gz >> test_mr_rosetta.com >> test_mr_rosetta.log >> Sorry: mr_rosetta failed... >> >> ******************************************************************************** Sorry, a subprocess has failed... >> >> END OF LOG FILE >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log : >> >> SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00 100.00 90.00 P 1 21 1 >> >> Scoring the model >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb Relaxing model at 3.0 A, generating and scoring 1 relaxed models >> >> Error message: >> >> child process stderr output: >> command: 'sh >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh' >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: >> line 3: 11915 Trace/BPT trap >> /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease @relax.flags > relax.log 2>&1 >> Failed to run RELAX >> >> >> ******************* ERROR ENDING *************** >> Failed to run RELAX ...see log file in >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log >> >> ******************* ERROR ENDING *************** >> >> >> The resulting log file showed the following: >> >> dyld: Library not loaded: >> /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib >> Referenced from: >> /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease >> Reason: image not found >> >> phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following: >> >> Running test_autobuild >> FALED TO RUN: test_autobuild >> ************************************************************** >> Error: test_command_line_rosetta_quick_test failed >> >> After running the resulting test_autobuild.com script, the log file showed: >> >> S_COORD_0001_ed_0005_ed.pdb >> averaged_map_coeffs.mtz >> coords1.pdb >> fobs.mtz >> relax.pkl >> seq.dat >> test_autobuild.com >> test_autobuild.log >> Sorry: Failed to run autobuild >> ERROR MESSAGE: >> Sorry the file >> /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file) >> >> >> The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation. >> >> I have two hunches for what could be going wrong, but I unsure how to fix either: >> >> 1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload page ;(. >> >> 2. The documentation also stipulates to specify a proxy server if behind a firewall using >> export HTTP_PROXY=proxyout.mydomain.edu:8080 >> I am behind a firewall, but on my machine there is no proxy server listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same. >> >> Thanks for all your help in advance and sorry that this is so long winded ;) >> >> Cheers, >> >> Joe >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

rosetta_mr autobuild failure
by Joseph Brock 02 Jun '11

02 Jun '11

Hi all, I wanted to use the rebuilding feature of Rosetta to help improve the R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8 installation was succesful, so after editing my .profile to include export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests: 1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up 2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta 3. phenix_regression.wizards.test_command_line_rosetta_quick_tests While the first was successful (ALL COMMAND_LINE TEST OK), the second reported the following error: Error: test_command_line_rosetta failed Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported: coords1.ali coords1.pdb fobs.mtz mr_rosetta_quick.eff perfect.mtz seq.dat test3.gz test9.gz test_mr_rosetta.com test_mr_rosetta.log Sorry: mr_rosetta failed... ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log : SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00 100.00 90.00 P 1 21 1 Scoring the model /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb Relaxing model at 3.0 A, generating and scoring 1 relaxed models Error message: child process stderr output: command: 'sh /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh' /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: line 3: 11915 Trace/BPT trap /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease @relax.flags > relax.log 2>&1 Failed to run RELAX ******************* ERROR ENDING *************** Failed to run RELAX ...see log file in /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log ******************* ERROR ENDING *************** The resulting log file showed the following: dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following: Running test_autobuild FALED TO RUN: test_autobuild ************************************************************** Error: test_command_line_rosetta_quick_test failed After running the resulting test_autobuild.com script, the log file showed: S_COORD_0001_ed_0005_ed.pdb averaged_map_coeffs.mtz coords1.pdb fobs.mtz relax.pkl seq.dat test_autobuild.com test_autobuild.log Sorry: Failed to run autobuild ERROR MESSAGE: Sorry the file /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file) The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation. I have two hunches for what could be going wrong, but I unsure how to fix either: 1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload page ;(. 2. The documentation also stipulates to specify a proxy server if behind a firewall using export HTTP_PROXY=proxyout.mydomain.edu:8080 I am behind a firewall, but on my machine there is no proxy server listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same. Thanks for all your help in advance and sorry that this is so long winded ;) Cheers, Joe

2 1

Setting phenix_env in ubuntu 10 system
by Jobichen Chacko 01 Jun '11

01 Jun '11

Dear All, I recently downloaded and installed phenix 1.7-1-743 on Ubuntu system. I need to run the command " source/usr/local/phenix**/phenix_env.sh" each time to launch the program when running as a command line. If I close that terminal and type the command in a new terminal, it is giving the reply "command not found". How does one set paths so that phenix.refine will be recognized in a new terminal window? I got some suggestiions to edit either ~/.bashrc or ~/.bash_profile and add the appropriate "source" command to it. But when I edit .bashrc phenix is automatically executed when I open a new terminal. I want to run phenix by typing command like "phenix.refine xx.pdb xx.mtz". Please let me know which file I should edit to get this. If possible can any ubuntu user send me a copy of the .bashrc file/or any other required file with environment path for phenix. Thank you for your time. Jobi

3 2

Autobuild Error
by B. Anand 01 Jun '11

01 Jun '11

Dear All, I am using autobuild to rebuild the model after MR. However, it stops with the following error which am I not able to comprehend. Could you please shed some light on this error. Am using phenix version 1.7.1 (Release tag:743). Thanks. With Best Regards, Anand *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_multiple_models: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/RUN_FILE_1.log : utoBuild Run 1 Tue May 31 01:00:15 2011 Build cycle 1 of 16 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 No refinement carried out (may need free R flags) Error message from phenix.refine: 'function' object has no attribute 'as_mtz_dataset' Refinement failed... *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_1_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/LAST.LOG may have additional information... 'function' object has no attribute 'as_mtz_dataset' ******************************************************************************** *************ERROR ENDING ******************* ******************************************************************************** *************ERROR ENDING ******************* -- B. Anand, Ph. D. Assistant Professor Department of Biotechnology Indian Institute of Technology Guwahati Guwahati 781039 Assam, India Email: banand(a)iitg.ernet.in anandbasub(a)gmail.com Phone: +91-361-258 2223 Fax: +91-361-258 2249 Web: http://www.iitg.ernet.in/banand/

2 1

Re: [phenixbb] Refining sucrose
by Yuri 01 Jun '11

01 Jun '11

All coot needs to run its real-space refinement is a .cif file as Nigel pointed out. You can also get this file from other ligand library websites (proDrg, hic-cup, etc...). The only catch here is. The name of your sucrose atoms must match, exactly, those in the file. Once you have such file go to the the file drop-down menu and click on Import CIF dictionary in coot. That should enable to rotate the rotatable bonds of your ligand -- Yuri Pompeu

5 5

heavy atoms
by ChenTiantian 01 Jun '11

01 Jun '11

Hi, I am dealing with a complex structure which the ligand contains a atom Iodine, I guess it's because Iodine is heavy atom, the electron density of Iodine turns red after 5 cycles refinement. Anybody coped with similar issue? How to let phenix know that the Iodine atom is part of the ligand? Best, Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

2 1

Phenix MTZ files,
by Saba Ferdous 154-FAS/BSBI/F05 01 Jun '11

01 Jun '11

Dear Phenix users I am new to Phenix..probably my question might be childish to you. so with appologies, I have predicted protein structure by using modeller, i want to refine my structure but i am unable to know that what is MTZ files n CIF files because i have only my PDB. And i want to fix beta deviations and outliers, bad angles and bad bonds in my structure. kindly help me and suggest me that what can i do to refine my structure. Best Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan

2 1

ligand cif file
by ChenTiantian 31 May '11

31 May '11

Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ? Best Regards, Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

3 3

mr_rosetta test failure
by Laurie Betts 31 May '11

31 May '11

We installed latest phenix and latest rosetta last week. I ran test script: phenix_regression.wizards.test_command_line_rosetta_quick_tests and got the test failing at the prerefine because of missing shared libraries, as shown below in the FAQ (italics). I tried again in both bash & csh after setting or exporting the environment variables shown below, but got the same exact error. If I do printenv the shell sees the new env var. What should I try next? THanks so much Laurie Betts & CD Poon University of North Carolina *Why does mr_rosetta bomb and say "error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory ? This may indicate that somewhere your system is defining the shared libraries that Rosetta needs, and these are for a place that is not where Rosetta expects them to be. You can try to ignore the previous definitions this way: If you are using the bash or sh shells: export PHENIX_TRUST_OTHER_ENV=1 or csh (C-shell): setenv PHENIX_TRUST_OTHER_ENV 1 in the script where you run mr_rosetta, or before you run it from the command line. *

2 1

Re: [phenixbb] strategy suggestion ???
by Michael Thompson 31 May '11

31 May '11

I once used the following strategy to search for ligands when the apo structure had already been determined. I was using Refmac at the time, but I don't see why you couldn't do it with phenix.refine. After you process your data, if your crystals with and without the ligands are isomorphous, then you don't necessarily need to do molecular replacement to get phases. After you process the data from your crystals with the ligands, you can take the mtz file and start refining with the pdb file for your apo structure. You can start with a rigid body refinement to account for any small shifts or rotations that may have taken place when you added the ligand. Then after that refine according to your protocol of choice. The main place you can run into trouble is if you have a polar space group. If you do the rigid body refinement and get a horrible R-factor, the there's a good chance you have indexed the two data sets in opposite orientations. This can be corrected by reindexing, I think the phenix tool for this is xmanip but someone can correct me if I'm wrong. Good luck, Mike ----- Original Message ----- From: "ChenTiantian" <chentiantian2010(a)gmail.com> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Monday, May 30, 2011 6:31:51 PM GMT -08:00 US/Canada Pacific Subject: [phenixbb] strategy suggestion ??? Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

1 0

strategy suggestion ???
by ChenTiantian 31 May '11

31 May '11

Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

4 3