- phenixbb - phenix-online.org

secondary structure restraint
by Jianghai Zhu 05 Jun '07

05 Jun '07

Hi all, I am refining a low resolution structure (~3.8 A). For some of the domains in the structure, we already have high resolution structures. Despite of some conformational changes in some loops, the core structures should be the same. I am wondering if it is possible to restrain the secondary structures in phenix.refine. Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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phenix.refine crashed
by Jianghai Zhu 05 Jun '07

05 Jun '07

Hi, In my refinement phenix.refine crashed with the following errors. ================================ xyz refinement =============================== Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1310, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 733, in refinement_machine h_params = h_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 136, in __init__ ignore_line_search_failed_step_at_lower_bound = True)) File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 242, in run log) File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 121, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 369, in compute_functional_and_gradients u_iso_refinable_params = u_iso_refinable_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 224, in compute_target sf_v3d_sel = sf_v3d.set_selected(self.hd_selection, [0,0,0]) RuntimeError: scitbx Internal Error: /net/sharptail/scratch1/rwgk/ auto_build/sources/scitbx/include/scitbx/array_family/boost_python/ flex_wrapper.h(473): SCITBX_ASSERT(a.accessor() == flags.accessor()) failure. What happened here? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Re: [phenixbb] elbow.builder
by William Scott 04 Jun '07

04 Jun '07

Problem solved: The OS X pre-compiled distribution comes with an executable gamess.Mar242007R1.x but the shell script seems to require gamess.00.x so in /usr/local/gamess I did this: sudo ln -s gamess.Mar242007R1.x gamess.00.x and benzene is as one would expect. BTW, when I run this under tcsh, I get a more informative error message -- it says it can't find gamess. Under zsh, it just says "Failed to read coordinates. Aborting optimisation." Anyway, it all works now. Thanks. Bill On Jun 3, 2007, at 3:08 PM, Peter Zwart wrote: > gamess is installed right? > > P > > > > 2007/6/3, William Scott <wgscott(a)chemistry.ucsc.edu>: >> actually, "small distortions" was too optimistic: >> >> http://chemistry.ucsc.edu/~wgscott/temp/benzene.png >> >> >> >> >> On Jun 3, 2007, at 2:33 PM, William Scott wrote: >> >> > Hi folks: >> > >> > I've been playing around a bit with elbow.builder, and found the >> > following: >> > >> > -------------- >> > >> > >> > elbow.builder --opt --smiles c1ccccc1 >> > >> > gives me a nice, flat, hexagonal benzene >> > >> > elbow.builder --gamess --smiles c1ccccc1 >> > >> > gives me a benzene that is slightly bent out of plane and has other >> > small distortions with respect to 6-fold symmetry. >> > >> > Is this a problem with elbow, a problem with gamess, or a Jahn- >> > Teller effect? >> > >> > >> > ------------ >> > >> > >> > >> > Also, I noticed elbow.doc requires a mozilla or netscape >> > executable. Since both of these are obsolete, maybe a firefox >> > executable should be an option? On OS X, "open" should open a URL >> > in the user's favorite browser, but it doesn't seem to work right >> > with Safari (which stupidly opens a Finder window of the directory >> > containing the html file). My workaround was to make a shell >> > script called "mozilla" that invokes Camino: >> > >> > #!/bin/zsh -f >> > /usr/bin/open -a Camino "$@" >> > >> > HTH someone. >> > >> > ------------------ >> > >> > >> > Bill >> > >> > >> > >> > >> > William G. Scott >> > >> > contact info: http://chemistry.ucsc.edu/~wgscott >> > >> > >> > >> > >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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elbow.builder
by William Scott 03 Jun '07

03 Jun '07

Hi folks: I've been playing around a bit with elbow.builder, and found the following: -------------- elbow.builder --opt --smiles c1ccccc1 gives me a nice, flat, hexagonal benzene elbow.builder --gamess --smiles c1ccccc1 gives me a benzene that is slightly bent out of plane and has other small distortions with respect to 6-fold symmetry. Is this a problem with elbow, a problem with gamess, or a Jahn-Teller effect? ------------ Also, I noticed elbow.doc requires a mozilla or netscape executable. Since both of these are obsolete, maybe a firefox executable should be an option? On OS X, "open" should open a URL in the user's favorite browser, but it doesn't seem to work right with Safari (which stupidly opens a Finder window of the directory containing the html file). My workaround was to make a shell script called "mozilla" that invokes Camino: #!/bin/zsh -f /usr/bin/open -a Camino "$@" HTH someone. ------------------ Bill William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott

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Binary file not executable during installation?
by lkemp＠mrc-lmb.cam.ac.uk 01 Jun '07

01 Jun '07

Hello BB I am trying to install Phenix on Suse 9.3. I went for the 2.6 version as i got this: 2.6.11.4-21.17-smp i686 when i typed uname. However it required libtermcap.so.2 so i switched to the 2.4 version as suggested on a previous BB query. This however also goes wrong: This time the binary.log file says that python in /common is not executable I checked and this was due to the need for libstdc++.so.6. I made a softlink directing this to the .5 version but it doesnt like this. Does anyone have any ideas??? Thank you in advance for any help Lauris

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AssertionError & TLS
by Kanchan Anand 01 Jun '07

01 Jun '07

Hello everybody, I am a new user of Phenix and presently trying to refine 3.6 A data of a protein-RNA complex. whenever i add tls into my .def file for the next run, i get this problem: Traceback (most recent call last): File "/data/software/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5 , in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/data/software/phenix-1.3b/phenix/phenix/refinement/command_line.py", li ne 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/data/software/phenix-1.3b/phenix/phenix/refinement/driver.py", line 130 8, in run log = log) File "/data/software/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 887, in refinement_machine h_params = h_params) File "/data/software/phenix-1.3b/mmtbx/mmtbx/refinement/adp_refinement.py", li ne 160, in __init__ tools.split_u(fmodel.xray_structure, tls_selections, offset) File "/data/software/phenix-1.3b/mmtbx/mmtbx/tls/tools.py", line 468, in split _u assert (u_iso < 0.0).count(True) == 0 AssertionError I have downloaded the new 1.3b version and without tls the program runs fine! could you please help Thanks in advance Regards kanchan

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textal problem
by Daniele de Sanctis 31 May '07

31 May '07

Dear all, I'm running textal.build to build a model in a 3.2 A map, and I'm using the option --input_model and --sequence. It seems to run ok until finishing the lookup but then i got the error message: doing sequence alignment against: ../pippo.seq sh: Syntax error: Bad fd number error: [Errno 2] No such file or directory: 'phentx-lookup-correct.pdb' indeed the file is not there, but i guess that is not there because o the previous Syntax error. any clue? thanks d -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartato 127 2781-901 Oeiras Portugal

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Re: [phenixbb] how to add phase info to the autosol wizard
by Tom Terwilliger 31 May '07

31 May '07

Hi Chuanbing, I'm sorry, that option isn't there yet! It is one that is on my list of to-do's. -Tom T At 01:51 AM 5/31/2007, CB Bian wrote: >Dear all, > > I am trying to add phase info from externally calculated > phases to the autosol wizard with S-SAD data. But I can not find > the option to do it in the running. Can someone help me? > > >Thanks in advance > >Chuanbing > >-- >ChuanBing Bian, Ph.D Student >Structural biology group >State Key laboratory of Structural Chemistry >Fujian Institute of Research on the Structure of Matter, >Chinese Academy of Sciences >155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China >E-mail: ><mailto:[email protected]>cbbian(a)gmail.com ><mailto:[email protected]>cbbian(a)fjirsm.ac.cn >Tel:(office)+86-591-8370-5814 ><http://protein.fjirsm.ac.cn/>http://protein.fjirsm.ac.cn >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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how to add phase info to the autosol wizard
by CB Bian 31 May '07

31 May '07

Dear all, I am trying to add phase info from externally calculated phases to the autosol wizard with S-SAD data. But I can not find the option to do it in the running. Can someone help me? Thanks in advance Chuanbing -- ChuanBing Bian, Ph.D Student Structural biology group State Key laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China E-mail: cbbian(a)gmail.com cbbian(a)fjirsm.ac.cn Tel:(office)+86-591-8370-5814 http://protein.fjirsm.ac.cn

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Re: [phenixbb] Death by Big-ass structure
by Petrus H Zwart 30 May '07

30 May '07

Hi Ulrich, Frank, Ralf has just placed a new version of cci_apps on our download sites (www.phenix-online.org). It contains a new application named phenix.xmanip (or mmtbx.xmanip if you only download the cctbx). It is basically a rewritten version of the reindex.py script I once wrote as an example jiffy. xmanip can read in various reflection files or mtz/cns data columns which subsequently can be used in reindexing or other tasks. The parameter file I send Frank a couple of days ago should still work, even though some rearrangements have been made . Typing phenix.xmanip reindex.def should do the trick. Other options are available as well. One could - generate map coefficients from a model (plain FC,PHIC, or sigmaA style maps if observed data is available) - get anomalous / isomorphous differences - scale two datasets together - generate symmetry mates of a model - the 'custom' option allows you to pass in a snippet of python code and have it executed. One has access to all datasets and molecular model read in. You could for instance add two datasets or multiply them if it makes you happy. Full documentation is under way. If you have any question, please let me know. Peter

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