- phenixbb - phenix-online.org

Refinement use of Friedel pairs
by Mark A Saper 11 Jul '07

11 Jul '07

I am refining a structure containing SeMet with data collected at peak wavelength. Provided I give the f' and f'', will phenix.refine calculate F+ and F- structure factors and use the provided FOBS+ and FOBS- ? CNS does this. Refmac only uses f' and I get >6 sigma Fo-Fc peaks on the Se. Thanks for your help. _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

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setting resolution for 2 datasets in AutoSol
by Thomas C. Terwilliger 10 Jul '07

10 Jul '07

Hi Luca, It's easiest to do this in 2 steps: 1a. You can set the resolution separately for each dataset in the AutoSol Wizard. In the GUI, just go through each dataset and set the overall resolution to your desired values as you go. Ignore the density modification and building that occurs in this run. 1b. Then you'll get an output exptl_fobs_phases_freeR_flags_2.mtz or equivalent that is phased to the resolution you specified, but that has all the data (with no phases) to higher resolution. 2. Now run the AutoBuild wizard, and set the resolution to your high-resolution limit. That should use the phases you generated, and include the high-res data for density modification and refinement. Equivalently, you can run AutoSol at low resolution then run AutoBuild at higher resolution by supplying an input_hires_file with the hires data. A key point here is that the building in AutoSol is just a preliminary build...the building in AutoBuild is the real thing. You can also run 2 datasets and set the resolution for each in a script. Here is a script to read in 2 SAD datasets and solve them together as one, setting the resolution of phasing to 3 A for the first and 2.9 for the second, cat two_datasets.inp input_seq_file seq.dat resolution 2.9 # Resolution expt_type sad input_file_list se.sca ############## NEW DATASET ################ run_list start # run "start" method. run_list read_another_dataset # starting a new dataset here resolution 3.1 # Resolution input_file_list br.sca Let me know if that does not do it! -Tom T >> From: lp212(a)mole.bio.cam.ac.uk >> Date: July 9, 2007 3:38:28 PM PDT >> To: phenixbb(a)phenix-online.org >> Subject: script for Zn and Se phasing >> Hi, >> I have collected two peak datasets on two different crystals, for a protein that contains zinc: >> 1. peak dataset at the Zn edge (lambda=1.285A, 2.5A reso) >> 2. peak dataset at the Se edge (lambda=0.98A, 2.8A reso) >> The protein has 2 Zn and 11 SeMet, and 4/au. When I input both >> datasets in the AutoSol GUI, Hyss finds correctly 8/8 Zn sites, and ~34/44 Se sites, but only when I cut back the resolution (4.2A for Zn, and 4.7A for Se). What I can't figure out is how to tell the Autosol GUI to use a low-res cutoff for finding the sites, and then use all the data for model building. Could someone please explain how to do this in the GUI, or send me a script? >> Thanks a lot! Apologies if this is trivial... >> Luca >

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Re: [phenixbb] depositing phenix-refined coordinates
by Ralf W. Grosse-Kunstleve 05 Jul '07

05 Jul '07

Hi Enrico, > However, I would be very grateful if someone could point me to the topic > already posted in the message below by Dr. Scott few days ago, > exactly at: > "a quick description for depositing phenix-refined coordinates?", > though the full message contained very interesting points I would > love to hear about We don't have a dedicated deposition tool yet, sorry. But we are actively working with the PDB on this. In the meantime, the .pdb files produced by phenix.refine are the best starting point. > (I also performed refinement by refmac/phenix, and observed kind of a > similar trend for those numbers). It may be because we are reporting mean deviations instead of root-mean-square deviations. This is kind of an oversight on our part and will be changed in the next version. Ralf

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CCI-Apps Verisons vs. Phenix Versions
by Schubert, Carsten [PRDUS] 05 Jul '07

05 Jul '07

Hi, Quick question about versions of CCI-Apps as standalones and in phenix. How does once decide which version of the CCI-Apps is more current? I have not looked in depth, but is there a equivalent build tag for the CCI-Apps in phenix as the one for the CCI-Apps. Currently I am assuming that the CCI-Apps are alway more up to date, but that may not hold true for the upcoming phenix 1.3 release. Thanks Carsten

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some general refine questions
by William Scott 05 Jul '07

05 Jul '07

Hi folks: With the helpful advice of the phenix crew, I've re-refined 2goz, an entry in the pdb in which I used refmac5 the first time around. There was a small error in the pdb: One nucleotide (C8 in chain A) was rotated 180 degrees about the glycosylic bond from where it should have been. The net result is one oxygen atom was in the wrong place in the structure, and this was apparent within the difference Fourier. After I rotated the base and re-refined in refmac, the Rfactor and other stats remained essentially unchanged (so this fix has nothing to do with the following): My refinement results in Refmac: REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.241 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1503 ; 0.009 ; 0.021 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2331 ; 1.676 ; 3.000 Then I refined in phenix. I get REMARK Final: r_work = 0.1737 r_free = 0.2224 bonds = 0.003 angles = 0.745 So the working and free R factor are both lower, and the geometry is substantially tighter. If I relax the weights in phenix, even to get rms bonds of around 0.006, the free-R goes up, which tells me this is not something I am justified in doing. Phil Evans once told me that anything tighter than about 0.01 (conservatively) was science-fiction, in that this is within the error of the idealized libraries for bond lengths. Other people have asked me about this too, and I didn't know how to reply. Is bonds = 0.003 angles = 0.745 realistic, or have I done something wrong? Even if I do structure idealization in Refmac, I can't get the rms bonds below about 0.005 (and my understanding is that it uses the same monomer library). Why is the weight multiplied by 0.5 by default? Since changing that to 1.0 slightly increases freeR, I assume it is the default for some reason. All the best, Bill PS: Could someone point me to a quick description for depositing phenix-refined coordinates? (The latest phenix installer seems to have omitted the docs.) William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott

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Re: [phenixbb] sugar links in phenix.refine
by Ralf W. Grosse-Kunstleve 04 Jul '07

04 Jul '07

Almost, but you need a separate scope (thing between braces) for each link, e.g.: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } refinement.pdb_interpretation.apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } Or alternatively: refinement.pdb_interpretation { apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } } Ralf

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Re: [phenixbb] Multivariate Z score L-test
by Claudia Scotti 29 Jun '07

29 Jun '07

Thank you so much. I'll try all the space groups and see what happens. Many thanks again, Claudia 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 ---------------------------------------- > Date: Fri, 29 Jun 2007 07:35:22 -0700 > From: PHZwart(a)lbl.gov > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Multivariate Z score L-test > > Hi Claudia, > > This could indicate that tyour data is actually P 2 1 1, P 1 2 1 or P > 1 1 2 or P 21 1 1, P 1 21 1, P 1 1 21. Try processing that data in > those spacegroups and see if that makes any difference. You might end > up havig to refine your structure in all spacegroups to find out which > possibility is the best. > > It could also indicate that the quality of your data is not very good, > either due to suboptimal data processing or because of bad diffraction > (or both). > > HTH > > Peter > > > 2007/6/29, Claudia Scotti : > > > > 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/ > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb _________________________________________________________________ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TX…

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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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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

1 1

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

2 1

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

1 0

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

1 0