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Multivariate Z score L-test
by Claudia Scotti 29 Jun '07

29 Jun '07

Dear List, I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44. I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. Matthews coefficient suggests two molecules per asu. No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent. When refining, refinement gets stuck as I mentioned above. I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data. Sorry for the probably trivial question and for probably missing important data. Thanks a lot for any help and suggestions, Claudia ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - /^2 : 1.827 - ^2/ : 0.838 - : 0.649 - , : 0.417, 0.242 Multivariate Z score L-test: 6.305 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 11.094 (correpsonding p value : 1.080e-01) The largest off-origin peak in the Patterson function is 11.09% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are no twin laws possible given the crystal symmetry, there could be a number of reasons for the departure of the intensity statistics from normality. Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems as well as bad data quality might be possible reasons. It could be worthwhile considering reprocessing the data. ----------------------------------------------------------------------------------------------- Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

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sugar links in phenix.refine
by Jianghai Zhu 21 Jun '07

21 Jun '07

Hi, How does phenix.refine handle the sugar links in refinement? I suppose phenix.refine will automatically recognize NAG and MAN. Will it recognized NAS-ASN, beta1-4, alpha1-4, etc linkages between sugars? 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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'Tasks' tab missing from 1.3b GUI and HL coefficients from a model
by Stephen Graham 21 Jun '07

21 Jun '07

Hi all, I recently (well, yesterday) installed the latest beta of phenix and everything is working great from the command line (which is how I use phenix 99.9% of the time). However, I fired up the GUI and found that the 'Tasks' tab appears to be missing from the 'Strategy Interface'. Is this a bug, a manifestation of an installation problem, or a feature? And... I was trying to use the GUI for prime-and-switch phasing to improve the maps for a partly-refined MR solution. What is the recommended path for creating HL coefficients from a model (from simulated annealing in phenix.refine) so that I can use the GUI's resolve 'prime-and-switch' strategy? Or is there an even better way of removing model bias and density-improving a big, low-res, MR-solved structure with 4-fold NCS in phenix? Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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harmonic restrains in phenix.refine
by Bjørn Pañella Pedersen 21 Jun '07

21 Jun '07

Hi all, Is it possible to use harmonic restrains in phenix.refine, in a manner similar to CNS v1.2? I have searched the phenix.refine documentation and the web, but can't find anything. I use version 2007_04_06_1210 of phenix. Thanks! -Bjørn -- Bjørn Pañella Pedersen Ph.D Student, MSc Department of Molecular Biology Office: +45 89425021 University of Aarhus Lab: +45 89425010 Gustav Wieds Vej 10c Email: bpp(a)mb.au.dk DK-8000 Aarhus C Lab WWW: http://www.bioxray.dk Denmark

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SAD + MR
by Lucas Bleicher 19 Jun '07

19 Jun '07

I have a dataset from a Cs-soaked crystal, and the protein has a domain solved in the PDB. The problem is that the map obtained just with the experimental phasing is not so easily interpreted, and the domain is just about 25% of the whole protein. Inspection of the map generated by MR suggests that it's a good solution, with residues fitting reasonably well on the density. Given the new features on Phaser 2.0, which I suppose is included in Phenix 1.3b, can anyone suggest a protocol to profit from both things (anomalous scattering + good search model)? Thanks in advance, Lucas ____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso

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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 08 Jun '07

08 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 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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