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question about SAD+MR
by crystallogrphy 24 Jul '09

24 Jul '09

Dear all, I have a Se-Met SAD data which diffracted to 2.8A (peak wavelength). The space group is P1. The map from SAD autosol and autobuild still gives crappy map, I can only see one continous alpha-helix density with all other density fragmented and difficult to identify. I suppose it is because of high mosaicity (1.5), low data redundency, and some radiation damage. Now I want to use mocular replace (sequence identify ~0.26) plus SAD data to give better map. 1. The result from MR is shown below and the density is poor as the sole SAD map: REMARK Log-Likelihood Gain: 121.374 REMARK RFZ=3.4 TFZ=100.0 PAK=0 LLG=29 RFZ=3.7 TFZ=5.4 PAK=0 LLG=69 RFZ=6.1 TFZ=4.0 PAK=0 LLG=97 RFZ=5.6 TFZ=5.0 PAK=0 LLG=118 LLG=121 2. I then tried to combine MR model and SAD data set phenix.autosol seq_file=zntb-sd.seq sites=14 atom_type=Se data=output-peak.sca sg="P1" cell="44.355 56.687 58.451 61.061 82.013 82.740" resolution=3.0 input_partpdb_file=AutoMR_run_1_/MR.1.pdb The program failed to run with such error message: Failed to carry out AutoSol_score_ha_solutions: [Errno 2] No such file or directory: 'AutoSol_run_3_/TEMP0/phaser_mtz.hand.mtz' I do not know where to get this phaser.mtz.hand.mtz file or how to generate it. Does anyone know? -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

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new gui on osx (10.5)
by Miguel Ortiz Lombardia 24 Jul '09

24 Jul '09

Dear all, We would like to run the new phenix GUIs from a remote computer. Both server and clients are OSX 10.5 (leopard) and they have the same versions of software (X11, python, phenix... all them pretty new versions) When trying to do so, we invariably get this error: This program needs access to the screen. Please run with 'pythonw', not 'python', and only when you are logged in on the main display of your Mac. I have searched the internet for similar problems and I found an old (one year) unresolved question on the same/similar issue: http://www.phenix-online.org/pipermail/phenixbb/2008-July/001129.html In our case, the /usr/local directory is not mounted over the NFS, it is local. As in that case, though, changing the LIBTBX_PYEXE_BASENAME to pythonw (for example in the phenix.autosol_gui wrapper) did not solve the issue. However, it is not clear to me that this variable has to be changed in a single place: it is found in many files. My question is: was this issue solved and I missed that? If not, anyone has a clue on how to solve the problem? Just to make it clear, the GUIs work perfectly locally in the server computer, that is, if not exported. Thanks a lot! Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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sigma cutoff
by dziuba＠amu.edu.pl 24 Jul '09

24 Jul '09

Hi, According to the Phenix manual, phenix.refine uses no sigma cutoff by default. Since I haven't changed this manually, why do I see in my pdb file MIN(FOBS/SIGMA_FOBS) 1.340? Thanks for help, Karolina

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ENSEmble parameters when the model is an EM map
by Peter Grey 24 Jul '09

24 Jul '09

Dear benevolent experts, I am trying to use Phaser for molecular replacement with EM-map as a model. The EM map, originally in a small P1 cell, was put in large P1 using CCP4's MAPROT and a mask that was defined by a certain cut-off level. Could you please advise me how to derive the EXTEnt and CENTre parameters needed for ENSEmble building ? Does the simple way of giving the size of the original P1 as the EXTEnt and its centre as CENTre sound reasonable ? I would be grateful for any advice and comments, Peter.

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anisotropic ADP factor refinement and optimize_wxc
by Joyce, Gordon M. (NIH/NIAID) [F] 21 Jul '09

21 Jul '09

Dear All, I have just recently started using phenix.refine and I hope I can get some advice. I am trying to refine my structure with anisotropic ADP factors while also optimizing the weighting parameters.When I give the following command, anisotropic refinement is carried out but optimization is not carried out as far as I can see (ie the rms bond and angles are not reduced, which is one of my concerns at the moment). phenix.refine protein1.pdb 072109checks.mtz ordered_solvent=true strategy=individual_adp adp.individual.anisotropic="not element H" optimize_wxc=true --overwrite pdb output values REMARK Start: r_work = 0.1952 r_free = 0.2388 bonds = 0.015 angles = 1.646 REMARK Final: r_work = 0.1413 r_free = 0.2448 bonds = 0.015 angles = 1.646 If I give the following command, optimization occurs and rms bond and angle values decrease. phenix.refine protein1.pdb 072109checks.mtz optimize_wxc=true --overwrite REMARK Start: r_work = 0.2048 r_free = 0.2388 bonds = 0.015 angles = 1.646 REMARK Final: r_work = 0.1917 r_free = 0.2352 bonds = 0.009 angles = 1.301 Is it possible to refine both anisotropic B factors and optimize ADP factors in the same run. Any advice would be great. Thanks, Gordon

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Phenix.refine coordinate error estimate discrepancies
by Phil Jeffrey 21 Jul '09

21 Jul '09

There seems to be a large discrepancy between the likelihood-based coordinate error estimate depending on whether the intensities or structure factor magnitudes are used, which doesn't make any sense to me. If I do: % phenix.refine rebuild.pdb data_withI.mtz phenix.refine picks up Imean and SigImean from the MTZ and refines the structure xray_data { file_name = "data_withI.mtz" labels = "IMEAN,SIGIMEAN" r_free_flags { file_name = "data_withI.mtz" label = "FreeR_flag" test_flag_value = 0 } then I get: | maximum likelihood estimate for coordinate error: 1.39 A But if I create an MTZ file without the intensities by using CAD on the original file, and use the same coordinate file: % phenix.refine rebuild.pdb data_withoutI.mtz phenix.refine picks up the structure factors instead: xray_data { file_name = "data_withoutI.mtz" labels = "F,SIGF" r_free_flags { file_name = "data_withoutI.mtz" label = "FreeR_flag" test_flag_value = 0 } } then this seems to be the right ballpark for a 1.75 Angstrom structure.... | maximum likelihood estimate for coordinate error: 0.28 A Similar R-factors, but there is a factor of 10 difference in the scale reported here: I's: r_work= 0.2266 r_free= 0.2570 ksol= 0.41 Bsol= 50.00 scale= 0.097 F's: r_work= 0.2221 r_free= 0.2557 ksol= 0.41 Bsol= 50.00 scale= 0.965 Version: 1.4 Release tag: 3 cctbx tag: 2008_12_07_1353 Platform: mac-intel-osx osx-10.5.6 User: phil Cheers, Phil Jeffrey Princeton

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Assertion Error when using kicked maps in solvent update
by Schubert, Carsten [PRDUS] 21 Jul '09

21 Jul '09

Hi In 1.4.106 I get the following Assertion Error when I use kicked maps (refinement.ordered_solvent.use_kick_maps=True) in the solvent update section: Traceback (most recent call last): File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/command_line/refi ne.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/refinement/comman d_line.py", line 89, in run call_back_handler=call_back_handler) File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/refinement/driver .py", line 1125, in run call_back_handler = call_back_handler) File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/refinement/strate gies.py", line 358, in refinement_machine log = log) File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/mmtbx/solvent/ord ered_solvent.py", line 205, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/mmtbx/solvent/ord ered_solvent.py", line 394, in find_peaks log = self.log) File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/mmtbx/find_peaks. py", line 98, in __init__ crystal_gridding_tags = fft_map.tags() File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/cctbx/maptbx/__in it__.py", line 152, in tags return crystal_gridding_tags(self) File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/cctbx/maptbx/__in it__.py", line 158, in __init__ assert gridding.symmetry_flags() is not None AssertionError Running from the same .def file w/o kicked maps works fine. Let me know if you need more info to debug this. Cheers, Carsten

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Duration of a phenix.elbow run
by Dirk 20 Jul '09

20 Jul '09

Hi, I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output: MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable phenix release (1.3) and the current version (1.4). Any help would be very appreciated Thanks Dirk

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Unable to produce kicked maps
by Schubert, Carsten [PRDUS] 17 Jul '09

17 Jul '09

Hi , I am trying to make some kicked maps in 1.4.106. At the end of the run all I am getting is Sorry: Duplicate mtz_label_amplitude FOFCWT Any workaround, except not to use kicked maps? Here the diff_params output for easer debugging. Cheers Carsten <<diff.def>>

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autosol
by sbiswas2＠ncsu.edu 16 Jul '09

16 Jul '09

Hi, I was trying to run autosol using gui however it crashed with the following message: Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT Is this again a version problem? I am running version 1.4-6 Any help will be appreciated, Shya

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rigid body refinement in phenix.refine
by Pavel Afonine 16 Jul '09

16 Jul '09

To PHENIX users who asked about this: I recall several people (unfortunately, I don't remember who exactly) asked me about the details of rigid-body refinement implementation in phenix.refine (MZ protocol) and I promised to let them know when the corresponding paper is published. So here it is: J. Appl. Cryst. (2009). 42, 607-615 Automatic multiple-zone rigid-body refinement with a large convergence radius P. V. Afonine, R. W. Grosse-Kunstleve, A. Urzhumtsev and P. D. Adams http://journals.iucr.org/j/issues/2009/04/00/dd5048/index.html Pavel.

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error message
by zachcp 15 Jul '09

15 Jul '09

A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks! SorryException : No array of observed xray data found. Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Xtriage.py", line 158, in OnExcept raise event.data SorryException: No array of observed xray data found.

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Average B-factor and ML error
by Leo Sazanov 15 Jul '09

15 Jul '09

Hi, phenix.refine outputs "WILSON B" value into PDB header after refinement, which is not the same as average B-factor of all the atoms in the structure, and not exactly the same as Wilson B-factor from SCALA scaling. How exactly is Wilson B-factor for phenix header calculated and would it be possible to output there also the average B-factor of all the atoms in the structure? Also, deposition into PDB requires only Luzzati coordinate errors, while phenix produces only ML based ones. Presumably ML estimate is better than Luzzati?, but it looks like often people just ignore PDB input for errors. It seems that it would it be useful in future to have ML option in the PDB submission process? Or should Phenix produce Luzzati errors as well? (I know that one can calculate av. B-fac in other programs or ask PDB to add some data to the deposition, but if the idea is to streamline the process...) Thanks, -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915 -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Anyone have a phenix.resolve script for after Phaser ?
by Phil Jeffrey 14 Jul '09

14 Jul '09

Although my usual m.o. is SHELX -> SHARP I'm exploring HYSS -> PHASER -> RESOLVE to see if the maps are any more interpretable. I think I've got good scripts for the first two steps but I'm not sure about my resolve script which stands at: phenix.resolve << EOD hklin myp3_auto.mtz LABIN FP=F SIGFP=SIGF PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD hklout resolve.mtz solvent_content 0.45 seq_file myp3.pir EOD This runs, but I could not tell from delving into the documentation if this was ideal or not. Thanks Phil Jeffrey (a Luddite and not using the GUI) Princeton

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Re: [phenixbb] refine occupancy of partially overlapping ligands
by Chris Ulens 14 Jul '09

14 Jul '09

Hi, I'm trying to refine the occupancy of 2 ligands that occupy the same binding pocket in 2 *partially* overlapping orientations. Let's assume I would define the ligands in 2 separate "chains" termed A and B. Could the experts point me to the proper syntax to define the correct group restraints to refine the occupancy? Thank you. Chris +++++++++++++++++++++++++++++++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium Tel +32 16 345812 Fax +32 16 345699 Telepathy 2.69 GHz +++++++++++++++++++++++++++++++

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can't find phaser_mtz.hand.mtz?
by Pei-Chun Lin 14 Jul '09

14 Jul '09

Hi, I am the beginner of crystallography and have a 3.5A map generated by MAD method using phenix GUI. I already traced and built 2/3 of my protein. I wish to use this partial model combined with SAD to generate a new map and see if the new map can help me to deal with the rest of the structure. Does it sound reasonable to you? However, after running AutoSol. I got this error message: Failed to carry out AutoSol_score_ha_solutions: [Errno 2] No such file or directory: 'AutoSol_run_1_/TEMP0/phaser_mtz.hand.mtz' What should I do now? Can't phenix automatically calculate it? PC _________________________________________________________________ Windows Live™: Keep your life in sync. Check it out! http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_012009

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tightening geometry
by Patrick Loll 10 Jul '09

10 Jul '09

Hi, I'm a little baffled. We have a 3 Å structure, and while the R values seem OK, I'd like to tighten up the rmsd values for the geometry. However, altering wxc_scale seems to have no effect. Specifics: In a clean directory, I run the following command phenix.refine X.mtz Y.pdb Z1.cif Z2.cif Z3.cif wxc_scale=0.??? strategy=group_adp (the cif files are libraries for different ligands) When I vary wxc_scale from 0.5 to 0.005, the geometry doesn't change at all, which makes no sense to me: For wxc_scale=0.5 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.05 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.005 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 ...you get the idea. These were run with phenix-1.4-3. With phenix-1.4-56, we get subtly different r values, but the bonds and angles numbers are the same as shown above (to 3 decimal places!), and the numbers don't change upon changing wxc_scale. Am I missing something here? Is there a better way to tighten up the geometry? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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Re: [phenixbb] source of fobs for refinement after AutoSol
by Tom Terwilliger 09 Jul '09

09 Jul '09

Hi James, Yes, that is correct. However if you want...you can just go on to AutoBuild and build a new model from scratch and generate a set of free R flags there, supplying your data as data=mydata.sca. I would recommend this anyway because AutoBuild makes a much better model than AutoSol, and including the model from AutoSol doesn't necessarily help (and can make it worse if the AutoSol model is really incomplete, such as from secondary- structure-only model-building). I use the AutoSol model-building just to see if things are going well and then I throw that model away. This is also the default when you use "after_autosol=True" in AutoBuild and when you run the AutoBuild GUI after running AutoSol. It is convenient to use the data and freeR in in exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to. The key of course is: once you refine a model and want to use that model further...you must use the set of free R flags used in that original refinement from then on. If you throw away that model and start from scratch you can also make a new set of free R flags. The hexdigest REMARK in your PDB file from phenix.refine helps you make sure that this is done correctly. All the best, Tom T On Jul 9, 2009, at 8:35 AM, James Whittle wrote: > Dear Tom: > > Ok. Thanks for the quick response! > > I should run then run AutoSol again to get this file, and it will > have the HL coefficients in it? > > --James > > > On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote: > >> Hi James, >> >> As you are expecting, in AutoSol the file >> exptl_fobs_phases_freeR_flags_*.mtz normally contains the >> experimental Fobs and free R flags for refinement, along with >> phases and HL coefficients from the experimental phasing. >> >> However if an anisotropy correction is applied to the data, then by >> default no refinement is done in AutoSol and no >> exptl_fobs_phases_freeR_flags_*.mtz file is created. This is to >> ensure that refinement is not carried out against anisotropy- >> corrected data (you want to refine against the original data, and >> have phenix.refine apply an anisotropy correction as part of >> refinement). >> >> If you supply >> >> input_refinement_file=my_data.sca >> >> then my_data.sca will be used for refinement and an >> exptl_fobs_phases_freeR_flags_*.mtz will be created. Note that >> my_data.sca can be identical to your input data file if you want. >> I am guessing that in your case an anisotropy correction was >> applied to the data in this way. >> >> I hope that helps! >> -Tom T >> ps. I am thinking of changing the default to make >> input_refinement_file automatically defined if an anisotropy >> correction is applied so that you don't have to do this... >> >> On Jul 9, 2009, at 7:55 AM, whittle wrote: >> >>> Dear all, >>> >>> I have a question regarding the output of AutoSol. >>> >>> I've run AutoSol, using the data directly from scalepack as a .sca >>> file, >>> and would like to now begin refining the structure I've built. >>> >>> There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the >>> AutoSol directory. Isn't this the right file to use? Since it's not >>> there, is it proper to use the phaser_2.mtz file for phenix.refine? >>> >>> --James >>> >>> _______________________________________________ >>> 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 >> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss >> >> >> >> >> _______________________________________________ >> 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 CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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source of fobs for refinement after AutoSol
by whittle 09 Jul '09

09 Jul '09

Dear all, I have a question regarding the output of AutoSol. I've run AutoSol, using the data directly from scalepack as a .sca file, and would like to now begin refining the structure I've built. There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the AutoSol directory. Isn't this the right file to use? Since it's not there, is it proper to use the phaser_2.mtz file for phenix.refine? --James

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2010 Gordon Conference on Diffraction Methods
by Andrew Leslie 02 Jul '09

02 Jul '09

The Gordon Research Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine, from July 18-23, 2010. As in the past, the program will include the latest developments in methodology covering all aspects of macromolecular crystallography, from crystallisation to model refinement and validation. We are currently preparing a preliminary program for the meeting, and would welcome suggestions for particular topics (with or without speakers). Please Email your suggestions to Andrew Leslie (andrew(a)mrc-lmb.cam.ac.uk) or Ana Gonzalez (ana(a)slac.stanford.edu). Andrew and Ana

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map output by phenix.refine
by 丁玮 01 Jul '09

01 Jul '09

Hi Pavel, Thank you for responding to my question so eloquently. But there are still something confusing me. First of all, when I used coot to open the "_map_coeffs.mtz", only two maps were displayed in the window,not four? Second, how to choose the maps coefficients? In phenix documentation, we konw that any specified coefficients can be set, for example: 2mFo-DFc, 2.7mFo-1.3DFc, Fo-Fc, 3Fo-2Fc. but it do not tell us why we should choose different coefficients. Thanks a lot. dream830106

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GUI problems
by Phil Evans 01 Jul '09

01 Jul '09

Hi I've just installed the Linux 64-bit version 1.4-105 on a CentOS5 machine, and I get a lot of errors in starting up the GUI. What am I missing? Also is it possible to install both the 32-bit & 64-bit versions together: I know it works for the executables in build/intel- linux-2.6 build/intel-linux-2.6-x86_64, but does that mess up the gui? It's OK on the command line Phil

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map output by phenix.refine
by Pavel Afonine 29 Jun '09

29 Jun '09

Hi Everyone, I think it's time to review this subject since it is one of the most frequently asked questions. Ironically, I think this is because we tried to make it as clear as possible -:) So, what kind of maps phenix.refine outputs by default? phenix.refine outputs two types of maximum-likelihood weighted maps (or, in other words, sigmaa-weighted maps): 2mFo-DFc and mFo-DFc. Now, as many of you noticed, the MTZ file with map coefficients "_map_coeffs.mtz" contains in fact four maps: 2mFo-DFc and mFo-DFc, and "filled" 2mFo-DFc and mFo-DFc (in fact fo-fc maps should be nearly identical; actually I have to fix it and not write identical fo-fc maps). The first two maps are computed using original Fobs (Fo), and the last two maps are computed using "filled Fobs", that is the original Fobs where missing reflections are "filled" with DFc. It is well known (I can spell a long list or references) that the data incompleteness affects the map quality, and sometimes, certain types of data incompleteness can *severely* distort maps. A possible solution (in order to reduce this negative effect) is to "model" missing Fobs somehow. One possibility is just to put in DFc in place where Fobs is missing, or as suggested by the classics, one can use <Fobs> taken in a resolution bin around a missing reflection. I even tried to use the random numbers and it was also better than doing nothing. Obviously, there is a nearly invisible line between the benefits of "filling in" missing Fobs and introducing bias. Where this line goes - is the subject of a research that to my knowledge is not done yet. Anyway, this is why phenix.refine writes out "regular" and "filled" maps: one is to give you unbiased but eventually lower quality map, and the other one is to give you a better-looking map with a risk of being biased. This way users have more options in exploring their maps (and less reasons for saying that Refmac produces better-appearing maps than phenix.refine -- see below). I have to mention that to my knowledge REFMAC always writes "filled" maps (those with missing Fobs substituted by DFc): - it is mentioned in Maria Turkenburg's thesis: http://www.ysbl.york.ac.uk/~mgwt/thesis-tth/chapter2.html#tth_sEc2.6.5 - and in Refmac docs: http://www.ccp4.ac.uk/html/refmac5/keywords/xray-general.html "Missing Data: For those reflections where the FP are missing, mFo is set equal to dFc. (...)". Correct me if I'm missing something. Please let me know if I wasn't clear in my attempt to explain this. I will update the phenix.refine documentation accordingly. Pavel.

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the different between 2mFo-DFc and mFo-DFc map
by 丁玮 29 Jun '09

29 Jun '09

hi,everybody, By phenix.refine outputde two likelihood-weighted maps: 2mFo-DFc and mFo-DFc.When they were displayed in coot, There is a vast difference between them, why? Thanks dream830106 　　　　　　　　dingding830106(a)sina.com 　　　　　　　　　　2009-06-30

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Autobuild requires more then 24 hrs to run on 32 cpu?
by Tatyana Sysoeva 29 Jun '09

29 Jun '09

Hello! I am trying to use Autobuild wizard and it seems that it takes longer time that I expected. That's why I have next questions: 1. What is "usual" time range estimate for Autobuild run with default parameters if my model has 7 chains with 284 aa in each? (if I'm running Autobuild on a single machine it does not finish in 3 days or on cluster with usage of 32 processors - in 24 hours) 2. Do I use phenix comman correctly for using several machines at once? I used /phenix-1.4-89, command line *phenix.autobuild data=e239a.hkl seq_file=seq.dat model=model.pdb nproc=32* In 24 hrs, which is my limit on cluster time, I get next things - AutoBuild_run_1_1_/AutoBuild_run_1_1.log ends with *Setting up to build 5 models to be combined into final model #1 NOTE: input model will be rebuilt in place: nothing will be added or deleted. Building 5 models ... Running up to 32 jobs in parallel... Splitting work into 5 jobs and running 32 at a time with csh in /home2/tas354/phenix_runs/20090610/1/AutoBuild_run_1_/TEMP0 Starting job 1... Starting job 2... Starting job 3... Starting job 4... Starting job 5...* AutoBuild_run_1_1_/TEMP0/AutoBuild_run_1_N.log ends with *Copying refined_pdb_in.pdb to composite_model.pdb in AutoBuild_run_1_/TEMP0 Beginning merge with current best model: refined_pdb_in.pdb Merging models: composite_model.pdb refine_1.pdb Refining model: Build_composite_3.pdb Model: AutoBuild_run_1_/TEMP0/Build_composite_refined_3.pdb R/Rfree=0.23/0.25 Rebuilding side chains from Build_composite_refined_3.pdb* or with error * TRIED resolve_extra_huge ...but not OK ******************************************************************************** Failed to carry out AutoBuild_build_cycle: ******************************************************************************** * Should I change parameters of the Autobuild which will dramatically reduce time for computations or should I ask for extension of my time for letting the programs to run as it is? I would give more details if it is needed I just could not think of some other right now. And I would appreciate any advices and suggestions! Thank you Tanya

2 2

phenix.refine simulated annealing modes
by Alejandro Buschiazzo 29 Jun '09

29 Jun '09

Dear Phenix users, I can't find information on the precise meaning of the different modes to perform SA during refinement; some choices are self-explanatory (such as "every_macro_cycle" or "second_and_before_last"), but what about "once" or "first_half"? (in my particular case, I want to perform only one simulated annealing routine on the second macro_cycle: can I use "once"? but, where should I define at which cycle to perform it?) Thank you for your help, Best, -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

2 1

questoin about AutoBuild
by crystallogrphy 27 Jun '09

27 Jun '09

Deal All, After I tried 9 runs of AutoSol from my MAD data by changing parameters (resolution, heavy atom numbers), I got 9 results, named as: AutoSol_run_1_ to AutoSol_run_9_. I found #9 and #7 have the lowest Rfree, so I want to pick the model from these two runs. However, when I use "phenix.autobuild after_autosol", the resulting AutoBuild files tell me that the program picked the result from #5 of AutoSol, not the lastest #9. Does anyone know how can I specify the exact number of AutoSol to run autobuild? I also tried this command "phenix.autobuild data=resolve_3.mtz model=overall_best.pdb seq_file=zntb-sd.seq"under the directory of AutoSol_run_9_, but failed with the following word: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_overall_best_edited.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... See AutoBuild_run_2_/LAST.LOG for more information Please resolve the R-free flags mismatch. ******************************************************************************** Does anyone know where is wrong? Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

2 1

"phenix.fobs_minus_fobs_map" new tool in PHENIX
by Pavel Afonine 27 Jun '09

27 Jun '09

Hi Everyone, for all of you who asked about computing Fo-Fo map in PHENIX: I added a new command line tool called "phenix.fobs_minus_fobs_map". For usage details just type phenix.fobs_minus_fobs_map and hit Enter, and it will print a couple of examples. Any feedback will be very appreciated. This is available in development version of PHENIX starting from 1.4-51: goto: http://www.phenix-online.org/download/ then click "Latest installers" under "Nightly builds (version 1.4-4 and above)" section. Pavel.

9 28

Refining partially occupied DNA on top of itself
by bschmidt＠berkeley.edu 26 Jun '09

26 Jun '09

Hello, I am having difficulty using Phenix to build and refine a DNA duplex. The issue is that my asymmetric unit consists of one protein monomer bound to DNA, but the protein is a dimer and the DNA is not palindromic, so each monomer is bound to a different sequence of DNA. As such, the density for the two different DNA half-sites is averaged out in the asymmetric unit. I have tried to place two duplexes directly on top of one another, each with 0.5 occupancy, and then refine. But I have noticed two problems. The first is that when xyz refinement is off, and I look at the output files, the density for DNA is awfully green, as if there were only *one* helix with 0.5 occupancy there. The other problem I noticed is that when I turn xyz refinement on, and look at the output files, one of the two half-sites gets moved several angtroms, so that it is in a region that generally has no density. I expect that, if done properly, the backbone of both half-site DNAs ought not to move. Any advice would be greatly appreciated. Thanks, Bryan Schmidt

4 7

multi-xtal averaging vs twinning
by Frank von Delft 26 Jun '09

26 Jun '09

Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement. 1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish) 2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too. 3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A). So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not. Or how *would* one approach this? Cheers Frank

4 7

Fix for autobuild/ligandfit problem with long $PATH
by Tom Terwilliger 25 Jun '09

25 Jun '09

Hi Phenix users, Several of you have had trouble with phenix.autobuild (or phenix.ligandfit) failing if you had a very long $PATH. The problem seems to be that if your $PATH is very long, then adding more to it and re-setting it can lead to a string that is too long (on some systems). Starting with PHENIX version 1.4-100 (today's version) you can add the keyword remove_path_word_list=" cns xiaroot ccp4 phaser" to shorten your $PATH. This keyword will selectively remove all paths from $PATH that include any of the words you specify, and that do not include the word "phenix", when running that phenix job. The log file will list what paths were removed. To figure out what paths to remove, type echo $PATH and choose the ones that identify other programs that are not part of phenix. I hope that will do it! Please let me know if this doesn't solve the problems. All the best, Tom T 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 CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

1 0

How to apply geometry regularization to selected residues in phenix.pdbtools
by Oliv Eidam 24 Jun '09

24 Jun '09

Hi, I was wondering if the geometry regularization in phenix.pdbtools can be applied to selected residues only. Something like: > phenix.pdbtools my.pdb selection="resname xyz" --geometry-regularization Many thanks in advance, Oliv -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eidamo(a)blur.compbio.ucsf.edu

3 2

pseudo translational symmetry
by youssef ben ammar 22 Jun '09

22 Jun '09

Hi all, I recently solved the structure of a protein containing 395aa using phenix autosol. After autoBuild I got about 65% of the sequence docked with 2 monomers in the ASU. After several refinement cycles the map has been improved and I build manually the remaining amino acids. But the problem is that R and Rfree didn't decrease below 0.28 and 0.33 respectively. I tried with NCS restraints, TLS but without success. When I revised phenix autosol logs carefully, I found that in xtriage the analyses of the Patterson function reveals a significant off-origin peak that is 41.59 % of the origin peak, indicating pseudo translational symmetry and no twin laws were found. The space group is P212121 (36.898, 59.45, 393.908, 90, 90, 90). The basic statistics suggested 1 copy in the ASU (but the solution gave 2 copies per ASU !!!). The same analysis done by ccp4i gave the same solvent content and math. coef. in p21212 but with 2 copies per ASU. In xtriage I found this suggestion: If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group P 21 21 2 (b-1/4,2*c,a) operator x, y+1/2, z unit cell of reference setting (393.91, 36.90, 29.73, 90.00, 90.00, 90.00) I am really stucked with the refinement and don't know how to deal with this pseudo translation. Any help or suggestions are welcome. Thank you. Youssef

3 2

density fit analysis in coot
by Raja Dey 22 Jun '09

22 Jun '09

Dear Friends, Can anyone tell what the number popping up against every bar of the density fit analysis histogram in COOT is? Is it a correlation co-eff between Fo and Fc or something else? I am interested to know how is this parameter calculated. One more question... Is it possible to build a model in COOT if only the electron density map and sequence is given? Although I know there are some programs to create an initial model. I am wondering whether COOT can do that. Thanking you in advance... Raja

2 1

error loading SHELXL HKLF4 reflection file
by jonathan elegheert 22 Jun '09

22 Jun '09

Dear phenix developers, I am using the one of the latest phenix.refine nightly builds, and I'm trying to load a SHELXL .hkl file into phenix; phenix.refine xxx_refine_004.def xray_data.file_name="/path/xxx.hkl"=hklf4 The "Iobs,SigIobs"labels are well recognized (so the "Merging symmetry-equivalent intensities" subroutine works ok), but the necessary "=hklf4" or "=intensities" appendage seems to cause problems. The strange thing is that in phenix.xtriage, the same command line flag works perfectly fine. Thank you for any pointers! Jonathan Elegheert PhD student Ghent University -------------- Traceback (most recent call last): File "/usr/local/phenix-1.4-95/phenix/phenix/command_line/refine.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 245, in __init__ log = self.log) File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 201, in __init__ self.raw_flags = self.extract_flags(data = self.raw_data) File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 266, in extract_flags parameter_scope = self.flags_parameter_scope) File "/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", line 566, in get_r_free_flags miller_arrays = self.get_miller_arrays(file_name=file_name) File "/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", line 406, in get_miller_arrays if (os.path.samefile(canonical_file_name, tabulated_file_name)): File "/usr/local/phenix-1.4-95/build/intel-linux-2.6-x86_64/base/lib/python2.6/posixpath.py", line 153, in samefile s2 = os.stat(f2) OSError: [Errno 2] No such file or directory: '/path/xxx.hkl=hklf4'

2 1

Re: [phenixbb] scaling
by Thomas C. Terwilliger 20 Jun '09

20 Jun '09

Hi, You can use autosol to do scaling of any pair of datasets, so if you just run the command below N times, once for each reference/to-be-scaled dataset pair you are interested in, it should do what you want: phenix.autosol native.data=native.sca deriv.data=deriv.sca correct_aniso=false skip_xtriage=true res_hyss=100 build=false this will stop with " HYSS failed...Probably no iso or ano differences.." because we are not giving HYSS any data. Then the file: AutoSol_run_1_/TEMP0/AutoSol_run_1_/TEMP0/mir_fbar.mtz will have the scaled native and deriv data in mtz format. For subsequent runs, the data will be in AutoSol_run_2_ ...etc I hope that helps! -Tom T >>> where ought i look for a phenx utility to scale any number of data sets >>> to >>> a reference data set? something akin to scale.inp in CNS. >> >> I don't think we have such a utility, unless there is something in >> solve (Tom?). -- But you shouldn't need this for any of the phenix >> applications. All trivial scaling of the scale.inp type is done >> on-the-fly. >> Ralf >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

1 0

scaling
by Bryan W. Lepore 19 Jun '09

19 Jun '09

where ought i look for a phenx utility to scale any number of data sets to a reference data set? something akin to scale.inp in CNS. -bryan

2 1

Can I limit the model's B factor range during refinement
by junfeng liu 18 Jun '09

18 Jun '09

Dear all, Several models have been refined using Phenix recently. It works well . But the model's B factors in some region are very high, higher than 150 or more. Of course, the wilson B is high too, about 60-70. I remembered that the B factor can be limited in the refinement using Refmac. Can I do the similar thing in Phenix ? Thanks in advance! Best wishes, leo

3 2

Molecular replacement
by Colin Levy 17 Jun '09

17 Jun '09

Within Phenix, is it possible to specify and lock the centre of rotation for a molecular replacement search. I have a single intrinsic anomalous scatterer within my protein which I can locate easily, therefore I would like to manually specify this point as the centre of rotation and then carry out a rotation search only about this single fixed point. Thanks for any suggestions, Colin

2 1

Re: [phenixbb] Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 Jun '09

Thanks a lot Nigel, I could generate new .cif file. Then I need to combine this ligand information while I am adding H atoms to model.pdb (protein+ligand). when I simply type "phenix.ready_set model.pdb" it will wrongly generate strange.pdb file. My question is how I can add this new geometry information (.cif file) while adding H atoms into modle.pdb file to make protein and ligand has H atoms in correct way. Thanks again in advace. YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 12:18:50 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand YoungJin If you opened the CIF in REEL you can right-click on the P-N bond and change the order to single. You can then use the menu Action -> Build -> Add Atom to add a hydrogen to the nitrogen by clicking on the nitrogen. Nigel On 6/16/09 9:03 AM, Young-Jin Cho wrote: Thanks Nigel, I opened ANP and truncated the terminal PO3 and ran phenix.ready_set. When I opened through phenix.reel, N atom has double bond to PB, thus has only one H atom, which I thought it should be single bond thus has two H atoms like any N6 of adenine. So if you can tell me how I can handle to put correct geometry, it will be great. Cheers, YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 11:21:18 AM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand Young-Jin You need to check that you and the PDB ligand database are talking about the same thing. You can see what the ligand ANP is by phenix.reel --chemical-components=ANP If you have the non-hydrogen atoms of your truncated ligand, phenix.ready_set will add the hydrogens and may even add the correct number of hydrogens to the terminal nitrogen. But what about its name? I would recommend find the three-letter code that corresponds to your ligand. Nigel On 6/15/09 7:01 PM, Young-Jin Cho wrote: Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat! _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

2 1

Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 Jun '09

Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat!

3 4

specification of column labels in command line promt
by Raja Dey 15 Jun '09

15 Jun '09

Dear Friend, I was trying to analyse one of my data set. I am getting the following error. Multiple equally suitable arrays of observed xray data found. Possible choices: Cam-pk-hr_scala1.mtz:IMEAN_pk,SIGIMEAN_pk Cam-pk-hr_scala1.mtz:I_pk(+),SIGI_pk(+),I_pk(-),SIGI_pk(-),merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Sorry: Multiple equally suitable arrays of observed xray data found. I have the following column labels in my .mtz file * Column Labels : H K L FreeR_flag F_pk SIGF_pk F_pk(+) SIGF_pk(+) F_pk(-) SIGF_pk(-) DANO_pk SIGDANO_pk IMEAN_pk SIGIMEAN_pk I_pk(+) SIGI_pk(+) I_pk(-) SIGI_pk(-) How I can specify column labels in a command line promt? Say, I want to use IMEAN_pk & SIGIMEAN_pk Thanks... Raja

2 2

phenix and PAE kernels
by nick＠silvaggi.com 15 Jun '09

15 Jun '09

Dear List, Sorry if this is a naive question, but is there a known bug with phenix (or python?) on PAE kernels? I have looked on phenix-online.org, but did not find anything. This problem is independent of the phenix version (I have tried 1.4-92, 1.4-3, 1.3, and several releases of cci_apps) and occurs with almost all of the programs (most fail in the cci_apps test_apps script). The problem appears to be specific to the PAE kernels, since the same programs run fine in the non-PAE counterparts. I am running Fedora 10 with kernel versions 2.6.27.24-170.2.68/PAE and 2.6.27.21-170.2.56/PAE. Phenix programs fail under both PAE kernels, but are fine under the non-PAE kernels. Thanks in advance for any help you can provide. Best regards, Nick Silvaggi long int too large to convert Traceback (most recent call last): File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/builder.py", line 10, in <module> from elbow.chemistry.any_chemical_format_reader \ File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/any_chemical_format_reader.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 16, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/utilities/monomer_utilities.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 4, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/mmtbx/mmtbx/refinement/print_statistics.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 1, in <module> # packaging File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 518, in <module> File "/usr/swr/cci_apps/cci_apps_sources/boost_adaptbx/boost/python.py", line 68, in __init__ OverflowError: long int too large to convert

4 5

phenix refine
by sbiswas2＠ncsu.edu 12 Jun '09

12 Jun '09

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J " ... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42 Does anyone know how to resolve this thanks, Shya

5 8

phasine error
by vennila Natesan 11 Jun '09

11 Jun '09

Dear members I am having solved strcutures for some five datasets of the same protein. All the cases autobuild builds ~97% of residues. I want to compare the phasing among those. Can we calculate the phasing error in the units of degrees in autosol? In all the cases, the Bayesian CC is between 45 and 56 and FOM is between 0.42 and 0.47.Is there any option in phenix to know the phasing error in degrees?

3 3

not enough memory error in Resolve/AutobuildWizard
by Tatyana Sysoeva 10 Jun '09

10 Jun '09

Hello! I'm trying to run AutobuildWizard on distant computer cluster. Runs failed. In Autobuild log file there is a message: *TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve ...NEED A BIGGER VERSION... TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve_huge ...NEED A BIGGER VERSION... child process stderr output: command: 'AutoBuild_run_1_/TEMP0/temporary.com' Sorry, not enough memory for RESOLVE ---------------------------------- TRIED resolve_extra_huge ...but not OK ******************************************************************************** Failed to carry out AutoBuild_set_up_build: ******************************************************************************** * Some Autobuild runs were ok, some stopped with that error message. What am I doing wrong? I installed Phenix1.4-3, locally to my home folder, run it from script file in queue. As I found this Linux computer cluster has next parameters - 1 login node: -Sun SunFire v20z 1U Rackmount Box -Dual 2.4 GHz AMD Opteron Processors -8 GB of ECC RAM Could you advise something to start with to find a problem? Sincerely, Tanya

8 11

Water/residue alternative conformations
by Roeland Boer 08 Jun '09

08 Jun '09

Dear all, I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)? The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13. I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } } Thanks, Roeland Boer.

3 5

Re: [phenixbb] autosol error 1.4-3 when trying to specify deriv.inano=noinano
by Thomas C. Terwilliger 06 Jun '09

06 Jun '09

Hi Francis, Thanks again for the files. They did help me debug the autosol wizard for this case. It turns out that on the command line you cannot say something like, native.data=nat.mtz native.labels="I SIGI" \ deriv.data=deriv.mtz deriv.labels="I+ SIGI+ I- SIGI-" deriv.inano=inano because only the first native.something= gets read, the others are ignored, and similarly only the first deriv.something= gets read. instead all this has to go in a parameters file, and then it all works fine. I have adjusted the wizard to catch this situation and to stop and tell the user that they need to use a parameters file to set more than one parameter in the native, deriv, or wavelength scopes. All the best, Tom T

1 0

coordinates and map shifted after phenix.refine without simulated annealing
by hari jayaram 06 Jun '09

06 Jun '09

Hi i am using phenix version 1.4 release tag 70 hari@charlie:~$ phenix.refine --version ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 70 Platform: intel-linux-2.6-x86_64 linux User: hari ------------------------------------------------------------------------------- I am seeing a strange shifting of my coordinates "out of my experimental phases map" before and after refinement without simulated annelaing I am at the final stages of my refinement. When I refine without simulated annealing the resulting model is shifted relative to my experimental phases map into which I build my model The phenix command line strategy i am using are rigid_body+individual_sites+individual_adp+tls .or the same strategy with simulated_annealing=true The output map coefficients fortunately match my model in both cases . But I am wondering why there is a difference. I am using the mlhl target for refinement to 3.1 A , My R and rfree is 28/31 . Any ideas why my model shifts without simulated annealing . All pdbs have the same CRYST record . I am using coot version 0.61 for my building and map display using fft inside of coot . hari

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Re: [phenixbb] coordinates and map shifted after phenix.refine without simulated annealing
by Thomas C. Terwilliger 06 Jun '09

06 Jun '09

Hi Hari, What is your space group? I am guessing that the shift is along an axis where the origin is not fixed, for example the b axis in P21. This could happen with rigid-body refinement where a molecule can move as a whole so that the center of mass could move along that axis. Perhaps someone else can comment as to whether there is or could be an optional term in phenix.refine to maintain the center of mass at the same coordinate in such cases. All the best, Tom T >> Hi i am using phenix version 1.4 release tag 70 >> >> hari@charlie:~$ phenix.refine --version >> ------------------------------------------------------------------------------- >> PHENIX: Python-based Hierarchical ENvironment for Integrated >> Xtallography >> Version: 1.4 >> Release tag: 70 >> Platform: intel-linux-2.6-x86_64 linux >> User: hari >> ------------------------------------------------------------------------------- >> >> >> I am seeing a strange shifting of my coordinates "out of my experimental >> phases map" before and after refinement without simulated annelaing >> >> I am at the final stages of my refinement. When I refine without simulated >> annealing the resulting model is shifted relative to my experimental >> phases >> map into which I build my model >> The phenix command line strategy i am using are >> rigid_body+individual_sites+individual_adp+tls .or the same strategy with >> simulated_annealing=true >> >> The output map coefficients fortunately match my model in both cases . But >> I >> am wondering why there is a difference. >> I am using the mlhl target for refinement to 3.1 A , My R and rfree is >> 28/31 >> . >> >> Any ideas why my model shifts without simulated annealing . All pdbs have >> the same CRYST record . >> I am using coot version 0.61 for my building and map display using fft >> inside of coot . >> >> >> hari >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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