- phenixbb - phenix-online.org

removing Van der Waals repulsion between two atoms
by Miguel Ortiz-Lombardía 06 Jun '07

06 Jun '07

Dear all, I've a question regarding phenix.refine. Is it possible in phenix.refine to remove repulsion between a couple of atoms to see to what distance they refine when unrestrained? I'm thinking in something like what in CNS/XPLOR one would do by setting: igroup interaction (selection1) (selection2) weights * 1 vdw 0. elec 0. end end I've been searching the web for a solution to this question, but haven't come up with anything. Sorry if I missed it! I would appreciate your help. Cheers, Miguel -- correo-e: ibdeno(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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Re: [phenixbb] how to add phase info to the autosol wizard
by Thomas C. Terwilliger 06 Jun '07

06 Jun '07

Hi again Chuanbing, I'm sorry, I mean 1.3b-d5 (d4 is just about to be released). -Tom T Hi Chuanbing, It will be available in version 1.3b-d4 which has yet to be released (or even built)...it takes a little time between the time I have put the code in and the time that it gets to you, unfortunately! -Tom T > Dear Tom, > > Thank you very much! It's expected! > I am using the Version 1.24.1b, is version 1.3 the next version you > mentioned? > > Chuanbing > > > > On 6/5/07, Tom Terwilliger <terwilliger(a)lanl.gov> wrote: >> >> Hi Chuanbing, >> >> I have added this to the AutoSol wizard >> (input_phase_file=my-phases.mtz) and the next version of PHENIX will have >> it. >> >> -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 >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > > -- > 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 > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] how to add phase info to the autosol wizard
by Tom Terwilliger 06 Jun '07

06 Jun '07

Hi Chuanbing, I have added this to the AutoSol wizard (input_phase_file=my-phases.mtz) and the next version of PHENIX will have it. -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 _______________________________________________ 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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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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