- phenixbb - phenix-online.org

Death by Big-ass structure&[email protected]
by Kate Kavanagh 13 Jun '07

13 Jun '07

Hi Peter, The reindexing works fine but when I try to convert back to R3:H all atoms with ANISOU records are given B-factors of -79.86: ATOM 1 N MET A 1 16.402 60.069 44.768 1.00-78.96 N ATOM 2 CA MET A 1 16.316 58.621 44.978 1.00-78.96 C ATOM 3 CB MET A 1 17.622 57.922 44.573 1.00-78.96 C ATOM 4 C MET A 1 15.966 58.300 46.432 1.00-78.96 C ATOM 5 O MET A 1 16.196 59.115 47.326 1.00-78.96 O ATOM 6 N PHE A 2 15.408 57.114 46.661 1.00-78.96 N ATOM 7 CA PHE A 2 15.047 56.686 48.013 1.00-78.96 C ATOM 8 CB PHE A 2 13.750 55.866 48.016 1.00-78.96 C ATOM 9 CG PHE A 2 13.323 55.436 49.391 1.00-78.96 C ..... And since TLS refinement has been used, all protein atoms have ANISOU records. Any suggestions? Kate

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Re: [phenixbb] [ccp4bb] DANO from PDB
by Peter Zwart 07 Jun '07

07 Jun '07

Hi Santosh, Here is an alternative to methods mentioned earlier. If you get the latest version of the cctbx or cci_apps (from www.phenix-online.org) you will find a new application named phenix.xmanip (or mmtbx.xmanip if you only download the cctbx). xmanip has some useful features, one of them is that one can provide pieces of python code to the interface that will be executed. You have full access to all cctbx methods available. Please find below an example parameter file that perform structure factor calculation (in less than 90 lines of code and input) that includes elements with f" and f' not being equal to zero (you have to set the values of f" and f' yourself rather then rely on lookup tables by wavelength) and allows you to set bulk solvent parameters such as ksol, bsol and the overall anisotropic B of the data (B_cart). Save the text below (between the hash-es in a file named params.def , change the unit cell and sg parameters, the input pdb file and f" and f' value dictionary to suit your needs: ( like fp_dict = { "S": 0, "C": 0 } fdp_dict = { "S": 0, "C": 2.8 } for instance } You can fool around with solvent density, solvent B, overall scale factor and overall anisotropic B value and resolution (d_min). Then run phenix.xmanip params.def and get a file named xmanip.mtz that will contain your error free data. If you want, you can add uniform or Gaussian errors yourself. Since xmanip is fairly new, you will find a bug in the current release that somehow appears when you do not read in any external xray data. This happens however right after the mtz file in question has been written out. This will be fixed in the forthcoming release (soonish). Let me know if anything is unclear or if you have trouble running it. HTH Peter Zwart ################################################################### xmanip { input { unit_cell = "80.127 80.127 71.582 90.00 90.00 120.00" space_group = R3:H model { file_name = tst.pdb } } parameters { action = reindex manipulate_pdb *manipulate_miller manipulate_miller { task = get_dano get_diso lsq_scale sfcalc *custom None output_label_root = "Imock" custom{ code = """ #------------------------------------------------------- # This you can change if desired # # Dictionary for fp and fpp values fp_dict = { "Zn": -0.189 } fdp_dict = { "Zn": 4.898 } # final resolution of the data d_min = 2.0 # anisotropic B value b_cart = [ 0, 0, 0, 0, 0, 0 ] # solvent parameters k_sol = 0.35 b_sol = 45.0 # overall scale k_overall = 1.0 #------------------------------------------------------- # below this point, things should be more or less okai # from mmtbx import f_model from cctbx.xray import observation_types #loop over all scatterers in the xray structure #print >> out, dir(xray_structure) scatterers = xray_structure.scatterers() for atom in scatterers.as_1d(): if fp_dict.has_key( atom.element_symbol() ): atom.fp = fp_dict[ atom.element_symbol() ] if fdp_dict.has_key( atom.element_symbol() ): atom.fdp = fdp_dict[ atom.element_symbol() ] #the changes have been made to fp and fdp #Now we have to do some trickery to get some fobs with bulk solvent #contribution ... #First make a 'fake' set of f_obs fake_f_obs = abs(xray_structure.structure_factors( d_min = d_min, anomalous_flag = True ).f_calc()) # make a 'fake' set of free flags fake_free_flags = fake_f_obs.generate_r_free_flags(fraction = 0.1, max_free = 99999999) fmodel = f_model.manager( xray_structure = xray_structure, r_free_flags = fake_free_flags, target_name = "ls_wunit_k1", f_obs = fake_f_obs, b_cart = b_cart, k_sol = k_sol, b_sol = b_sol, overall_scale = k_overall ) # now get the final values of F+ and F-. # Note the abs to get amplitudes only result = abs( fmodel.f_model() ).set_observation_type( observation_types.amplitude() ) # you want make this into intensities? result = result.f_as_f_sq() # lets leave the intensities alone for now, and just make 'mock' sigmas # to statisfy certain programs. # Don't forget to set the observation type! sigmas = result.data()/100.0 result = result.customized_copy(data = result.data(), sigmas=sigmas).set_observation_type(result) #By default, a parameter named result is passed back to the xmanip #routines and will be written to the final mtz file """ } } } output { logfile = "xmanip.log" hklout = "xmanip.mtz" xyzout = "xmanip.pdb" } } ################################################################### Santosh Panjikar wrote: > Hi all, > > Does anybody have a program which can calculate anomalous differences or > F+ and F- from a refined structure at given wavelength and resolution ? > > Thanks > Santosh > > > Santosh Panjikar, Ph.D. panjikar(a)embl-hamburg.de > Staff Scientist > EMBL Hamburg outstation http://www.embl-hamburg.de/~panjikar/ > DESY, Notkestrasse 85 Tel.:+49-40-89902-141 > 22603, Hamburg, Germany Fax: +49-40-89902-149

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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 05 Jun '07

05 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 05 Jun '07

05 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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