- phenixbb - phenix-online.org

changes from 1.8.1-1161 to official 1.8.1?
by Eric Williams 02 Oct '12

02 Oct '12

Where any major bugs fixed between the 1161 nightly build and the official 1.8.1 release? I have a large batch job running that uses 1161. If the squashed bugs are big enough, it might be worth stopping the job to install the new release. Otherwise, I'll just let it run to completion. Thanks. :) Eric

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Phenix version 1.8.1 released
by Paul Adams 01 Oct '12

01 Oct '12

The Phenix developers are pleased to announce that version 1.8.1 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - New GUIs: phenix.find_alt_orig_sym_mate General: ======== - Multiple bug fixes - New commands: phenix.erraser, phenix.merging_statistics - Added geometry restraints for over 400 non-standard amino acid entries Refinement: =========== - Overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior) - Improvements to torsion NCS rotamer correction - Real-space refinement (including rotamer fitting) for twinned data New command: ============ - phenix.erraser: - New method from Fang-Chieh Chou and Rhiju Das (Stanford) combining Rosetta nucleic acid rebuilding with phenix.refine (requires separate installation of Rosetta 3.4 or more recent) Molecular Replacement: ====================== - Phaser updated to version 2.5.2: - Scattering from HETATM records that represent modified amino acids (e.g. MSE/SeMet) included so that maps no longer show holes for these HETATM records in the model; occupancies will not be reset. - Packing test was incorrectly applied to reoriented molecules where there was PTNCS Experimental Phasing and Model Building: ======================================== - AutoSol: - Scale of derivative in SIR (for RIP phasing) can be set with keyword "derscale" - AutoBuild: - Unassigned chains are now given the segid of "UNK" and are normally given chain ID="U" Ligands: ======== - eLBOW: - New option, --multiple-planes, to generate planes around double bonds - Saturated rings now have dihedral restraints to maintain chair conformation - REEL: - View relationships between ligands using PubChem fingerprint and tanimoto score. Miscellaneous: ============== - phenix.real_space_correlation: - Simplified command-line behavior - phenix.merging_statistics (new command): - Calculate statistics for unmerged data in a variety of formats, including <I/sigmaI>, R-merge, R-meas, R-pim, CC1/2 - References: Diederichs K & Karplus PA (1997) Nature Structural Biology 4:269-275 Weiss MS (2001) J Appl Cryst 34:130-135. - phenix.kinemage: - Improvements to handling of alternate conformations. - phenix.combine_models: - Combine two models, taking the best parts of each to create a new model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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point-n-click installer is bjorking OS X Dock
by Scott Classen 26 Sep '12

26 Sep '12

Hello, After running the OS X point-n-click installer for the 1.8.1-1160 nightly build, the dock becomes unresponsive and I can no longer command+tab to switch between applications. I've reproduced this on 2 Macs. One running 10.8.2 and the other running 10.7.5 Relaunching Finder does not fix the proton dock/app switching Logging out and then logging back in fixes the problem. Scott

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den refinement with multiple reference files
by Andreas Förster 26 Sep '12

26 Sep '12

Dear all, I've started DEN refinement on a structure obtained by MR from data optimistically going to 3.8A. There are several chains of two kinds in the structure. High-resolution structures exist for both. How do I use two reference files for DEN refinement, and how do I assign which chain corresponds to which reference? (Currently, I'm using reference_file = None.) Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Phenix cut out density labels choice
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following issue with running Phenix.cutout density either on command line or in GUI. I have multiple columns in the mtz.file and I want to choose map coefficients FOFCWT_d1-8,PHFOFCWT_d1-8 for the difference map to be cut around pdb selection. I run a command: phenix.cut_out_density model.pdb my.mtz cutout_fix_position=True cutout_model_radius=10 cutout_type=model \ map_coeff_labels=FOFCWT_d1-8,PHFOFCWT_d1-8 Problem: The output cutout.mtz has FWT and PHWT (which I did not have at all in the input) and not my difference map coefficients, and obviously the map is not my difference map. In GUI is the same problem, I choose columns I need but it outputs FWT and PHWT again. Please, let me know what I am doing wrong. Thank you very much! Mikalai

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Combine map labels
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following question. I have generated several Fo-Fc sa omit maps (FOFCWT, PHFOFCWT) for different portions of a DNA molecule. Now that I have each omit map as a separate file to display the whole DNA omit map I have to load them in coot one by one. Is there a way of how to combine all this maps into one file and have a single name for label columns so that the whole map will open at once? I managed to put them all in one file but column labels are separate: FOFCWT_1, PHFOFCWT_1 FOFCWT_2, PHFOFCWT_2...... Can they all go under FOFCWT, PHFOFCWT? Thank you very much for any suggestion Mikalai

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Specifying union of two chains in pdb_atom_selection
by Francis E Reyes 20 Sep '12

20 Sep '12

Hi all, I issue the following command to pdb_atom_selection but I get 0 atoms selected at the end? $ phenix.pdb_atom_selection refine_to_submit.pdb "chain X and chain B" refine_to_submit.pdb Monomer Library directory: "/usr/local/phenix-1.8-1069/chem_data/mon_lib" Total number of atoms: 3817 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} Chain: "X" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} chain X and chain B 0 atoms selected Thanks! F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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Scaling for Isomorphous Difference Maps
by Michael Thompson 20 Sep '12

20 Sep '12

Hello All, I'm currently using the GUI to calculate some Fo-Fo isomorphous difference maps. From looking at the Phenix documentation, it hasn't become apparent to me if the tool that performs this calculation automatically scales the two sets of amplitudes to one another, or if the input mtz files need to be scaled together elsewhere before running the map utility. Any info would be appreciated! Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Two versions of TFZ, molecular replacement
by 赵岩 19 Sep '12

19 Sep '12

Hi everyone, I am trying to solve a structure though molecular replacement and I have obtained a suspected solution. The header of the solution as follows, REMARK TITLE [no title set] REMARK Log-Likelihood Gain: 238.884 REMARK RFZ=10.9 TFZ=13.9 PAK=2 LLG=235 TFZ==5.0 LLG=239 TFZ==5.0 REMARK ENSEMBLE 1 EULER 15.53 0.10 344.54 FRAC -0.499 -1.000 -0.499 At first sight, the solution has no problem(TFZ>8), but the second and third TFZ are very low. For a correct solution, the later TFZs always higher than the first TFZ. So I don't konw how to understand the later TFZs and what extent I can refer to them. Thanks a lot! --

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advice for speeding up cif_as_mtz
by Eric Williams 19 Sep '12

19 Sep '12

I'm currently running cif_as_mtz and model_vs_data on the whole PDB as part of my dissertation. Time has become a critical concern, and cif_as_mtz (dev-1141) is running very, very slowly (1-4 minutes per entry). Here's how I'm calling it: phenix.cif_as_mtz <sf_cif_fn> --ignore-bad-sigmas --merge --remove-systematic-absences --map-to-asu --symmetry=<pdb_model_fn> --output-file-name=<sf_mtz_fn> I'm hoping that perhaps someone could help me determine which command line argument(s) could be removed to provide maximum speed-up. Thanks. :) Eric

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B-iso vs. B-aniso
by Yuri 18 Sep '12

18 Sep '12

Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable R-gap, for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts/opinions/call-outs from the community are welcome. Cheers, -- Yuri Pompeu

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Monitoring MR_ROSETTA progress on a cluster
by Dmitry Rodionov 17 Sep '12

17 Sep '12

Hi Tom, How are you doing? Sorry to bother you again. I got my hands on a login to local cluster (MOAB) and started MR_rosetta there as well. Problem is, I have hard time figuring out what it is doing at this moment and if everything is under control. All I see in the queue are the original submission and a process it spawned less then a minute later. While a day ago there were 30 processes (that's how much I can have). All mr_rosetta.log files end with a list of methods to be run. MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/LIST_OF_JOBS_RUNNING says: /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1 /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log MISSING FINAL COUNT: 0 But the file happily exists : GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log .... Starting job 1000...Log will be: /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1000.log And that job successfully finished a while ago. Is everything ok with the run? Am I just being impatient? Thanks! Best regards, Dmitry

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Custom restraints editor
by Kristof Van Hecke 17 Sep '12

17 Sep '12

Dear, When I try to define additional 'planarity' restraints via the 'Custom restraints editor', I get the following error (see below): (I'm using the Phenix nightly build dev-1148 on a Mac Book Pro, OS X 10.5.8, but had the same problem with the official release version 1.8) I also tried to add these additional restraints to my restraints .cif file, but then rmsd values increase to unreasonably high values. (I just want to keep 2 chlorine atoms on a phenyl ring better in the same plane) Any ideas please..? Thank you very much Kristof Van Hecke --------------------- untimeError : Syntax error: missing closing quote (python_object, line 1) Traceback (most recent call last): File "/Applications/phenix-dev-1148/phenix/wxGUI2/Programs/Refine/ Dialogs.py", line 296, in OnUpdate new_phil = self.GetPhilObject() File "/Applications/phenix-dev-1148/cctbx_project/wxtbx/ custom_restraints.py", line 646, in GetPhilObject new_phil = self._index.master_phil.format(python_object=self._params) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1714, in format result.append(object.format(sub_python_object)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1714, in format result.append(object.format(sub_python_object)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1714, in format result.append(object.format(sub_python_object)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1727, in format result.append(object.format(sub_python_object_i)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1727, in format result.append(object.format(sub_python_object_i)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1094, in format words = type_as_words(python_object=python_object, master=self) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 151, in as_words source_info="python_object") File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 60, in tokenize_value_literal tokenizer.settings(contiguous_word_characters="")])) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ tokenizer.py", line 249, in next where_str(O.source_info, char_iter.line_number))) RuntimeError: Syntax error: missing closing quote (python_object, line 1) Platform info: __FILE__ = /net/patchnose/scratch1/phenix/phenix-dev-1148/ cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Sep 3 2012 __TIME__ = 06:05:56 __i386__ __APPLE_CC__ = 5367 __GNUC__ = 4 __GNUC_MINOR__ = 0 __GNUC_PATCHLEVEL__ = 1 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_51 PY_VERSION = 2.7.3 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: 79991 os.name: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-9.8.0-i386-32bit platform.architecture(): ('32bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 2 Memory total: 4,294,967,296 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = √Ö

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Sa_Omit_map_DNA_low_resolution
by Mikalai Lapkouski 15 Sep '12

15 Sep '12

Hello, I want to generate a simulated annealing omit map around DNA molecule in my protein-DNA complex for publication. My resolution is very low - 5A. 1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part) from pdb and ran phenix.refine with simulated_annealing=True. But resulted Fo-Fc in the omitted region is very weak. Is it because of the low resolution and because big part of the model was omitted? 2. Next, I wanted to generate a composit_sa_omit map as in this case DNA would be deleted in small portions and the resulted map would give me a map I can use for publication: phenix.autobuild data=inp.mtz model=whole.pdb (contains DNA) maps_only=True (to skip rebuilding) composite_omit_type=sa_omit omit_selection=DNA.pdb (contains only DNA coordinates). But the job runs too long and still it seems like it is doing rebuilding. Is this a correct command and correct action to create a sa_omit map for the DNA in my complex? Thank you a lot for the help, Nick

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Re: [phenixbb] Two versions of TFZ, molecular replacement
by yzhao 14 Sep '12

14 Sep '12

Hi, Some information may be needed. The model used to do molecular replacement is not an original homolog PDB file. I feed the homolog structure and sequence alignment to MR_rosetta, and I obtained an overall_best.pdb from AutoBuild(diffraction resolution is about 3. 5A). So I use this overall_best.pdb to run Phaser, and achieved a solution as I just mentioned. the overall_best.pdb from AutoBuild has no obvious regular secondary structure relative to the homolog structure, but their overall appearances are very similar. Before I run Phaser, I also checked native Patterson, there is no large off- origin peak. Additionally, the self rotation function and matthews_coef indicate there is a monomer in ASU. Thanks a lot! -- Yan Zhao Randy Read 写:Hi, There's an explanation of the TFZ== entry and how to interpret the job history on our web page:http://www.phaser.cimr.cam.ac.uk/index.php/ Molecular_Replacement#Has_Phaser_Solved_It.3F Basically, the TFZ=13.9 means that, in the translation search using the orientation that came from the rotation function, the Z-score of this peak was 13.9. However, we found that the TFZ was too sensitive to random errors in the orientation, so Phaser now computes what the TFZ score would have been if the orientation in the translation search had been the optimised one from the rigid- body refinement. (We call this the TFZ-equivalent, denoted as TFZ==.) So after the refinement (giving LLG=235), a random sampling of translations shows that the TFZ score would have been 5.0 for the refined orientation. The next two entries are the LLG after the final refinement at full resolution (239) and the TFZ score for that refined solution (again 5.0). What you see is very unusual behaviour. The TFZ -equivalent is almost always higher than the original TFZ, and I can't recall a case where it was significantly lower. One possible explanation occurs to me. If your crystal has translational NCS ( indicated by a large off-origin peak in the native Patterson) and you're searching for a dimer, a translation search with the dimer axis parallel to a crystallographic 2-fold would give a very sudden increase in the LLG when the dimer is in the right place relative to the crystallographic 2-fold to generate a model that obeys the translational NCS. Then, if the refinement changed the orientation of the dimer so that its axis was less parallel to the crystallographic 2-fold, that would reduce the modulation of the calculated data and reduce the TFZ. If these are the circumstances of your job, then you should be able to fix it by making sure that you have a recent version of Phenix, then running a job looking for 2 copies of the monomer. In that case, Phaser will take proper account of the translational NCS and there won't be any strange artefacts. If those aren't the circumstances, then I'm very puzzled and would appreciate receiving the data, model and other information needed to reproduce your job ( off-line) to check out what is going on! Best wishes, Randy Read On 14 Sep 2012, at 20:13, 赵岩 wrote:Hi everyone, I am trying to solve a structure though molecular replacement and I have obtained a suspected solution. The header of the solution as follows, REMARK TITLE [no title set] REMARK Log-Likelihood Gain: 238.884 REMARK RFZ=10.9 TFZ=13.9 PAK=2 LLG=235 TFZ==5.0 LLG=239 TFZ==5.0 REMARK ENSEMBLE 1 EULER 15.53 0.10 344.54 FRAC -0.499 -1.000 -0.499 At first sight, the solution has no problem(TFZ>8), but the second and third TFZ are very low. For a correct solution, the later TFZs always higher than the first TFZ. So I don't konw how to understand the later TFZs and what extent I can refer to them. Thanks a lot! -- _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------Randy J. ReadDepartment of Haematology, University of CambridgeCambridge Institute for Medical Research Tel: + 44 1223 336500Wellcome Trust/MRC Building Fax: + 44 1223 336827Hills Road E-mail: rjr27(a)cam.ac.ukCambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Anisotropic scale matrix in phenix.refine
by Alex Taylor 13 Sep '12

13 Sep '12

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Ligand geometry, Ideal vs. Observed
by Yuri 12 Sep '12

12 Sep '12

Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show is the geometry of the ligand, bond angles/lengths, dihedrals, etc... One of my models has a hi-res of 1.18A and the ligand density is really clear and complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot -- Yuri Pompeu

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Bond/Angle restraints for multiple copies of ligands/cofactors
by Eckhard Hofmann 12 Sep '12

12 Sep '12

Hi all, if the xray data reach real atomic resolution (say <1A), one can nicely refine cofactors w/o restraints. In intermediate cases, the existence of multiple copies allows to use the "SAME" option in SHELX refinement to restrain identical molecules to each other, somewhat like NCS, but on bonds and angles. Is there a possibility to do something similar with PHENIX? I have structures with up to 16 or more copies in the ASU (and several copies per chain), and 1.1A resolution. This would give me a very stable way to access unbiased information about stereochemistry. (Using NCS is of course not an powerful idea, as the torsion angles might vary between the different copies). Thanks for feedback, Eckhard -- Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> Ruhr-Uni Bochum AG Proteinkristallographie, LS Biophysik, ND04/316 44780 Bochum Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762

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Advice on final refinement of twinned R3 structure: DETWIN and ML-target vs twin_lsq_sq target
by Bjørn Panyella Pedersen 10 Sep '12

10 Sep '12

Dear list I would like some advice on how to do the final refinement of a twinned structure: I have a 3.0A structure (sg R3) which is twinned. I have collected ~50 datasets and the estimated twin-fraction varies from 0.2 to 0.45 based on phenix.xtriage analysis (britton plot etc). The structure could only be solved by experimental phasing using _detwinned_ datasets (detwinned by the ccp4 program DETWIN). Refinement of the model was initially done using my highest resolution _detwinned_ dataset (3.0A, britton_alpha:0.21) and a ML target in phenix.refine. Lately I have switched to th twin_lsq_f target and refined using the 'unmodified'/twinned dataset. 1. I have tried systematically to detwin the dataset with different twin-fractions and then refine using the ML-target and my best refinements comes using an alpha of 0.2 (see attached figure). This fits the Britton plot etc. 2. xtriage estimated the twin-fraction to by ~0.21, but using twin_lsq_f, phenix.refine now gets alpha to be 0.31. This seems like a large increase to me? 3. Using the manually detwinned dataset and a ML-target gives better R-factors than using the twin_lsq_f target (see attached figure). Bottom line: How should I report/deposit this structure: A. Should I use the manually detwinned data and an ML-target to get a model that explains the data best (lowest R-factors). And deposit my structure with modified (i.e DETWINNED) structure factors. I fear that people would react strongly to the deposition of modified F_obs in the pdb. I could deposit both twinned and detwinned structure-factores but this might also confuse? OR B. Should I use the twin_lsq_f target and accept that my deposited model is not as good as I know it could be. And deposit my structure with the real (i.e TWINNED) structure factors. OR C. Something I'm not aware of means that refinement using the ML-target is not allowed on detwinned datasets, causing me to have artificially low R-factors. I hope I'm not missing something basic here.:) Thank for any advice, pointers and ideas! -Bjørn -- Bjørn Panyella Pedersen, PhD Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco MC2240, 600 - 16th Street S414 San Francisco, CA 94158-2517 Phone: +1 415-476-3937 E-mail: bjopp(a)msg.ucsf.edu http://www.msg.ucsf.edu

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error message on dev-1145 during den session
by fulvio saccoccia 07 Sep '12

07 Sep '12

Dear Phenix users, here you have an error occurred during a DEN refinement cycle on a twinned structure. Please, help me in order to overcome the problem. This is the command line I used to run phenix: phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50 convert_to_isotropic=true xray_data.high_resolution=3.6 nproc=4 secondary_structure_restraints=true optimize_xyz_weight=true optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb use_geometry_restraints=true den.params fix_rotamers=true den.params is attached I was running phenix dev-1145 on a 64bit Debian machine. This is the error message: Running DEN torsion optimization on 4 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 100.0 ...trying gamma 0.2, weight 100.0 ...trying gamma 0.0, weight 300.0 ...trying gamma 0.2, weight 300.0 Traceback (most recent call last): File "/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module> den_refine.run(command_name="phenix.den_refine", args=sys.argv[1:]) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py", line 113, in run customized_master_params=master_phil) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py", line 146, in run call_back_handler=call_back_handler) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py", line 1532, in run ncs_manager = self.ncs_manager) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py", line 830, in refinement_machine log=log) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line 88, in __init__ "serious error; please contact bugs(a)phenix-online.org.") % so) RuntimeError: DEN weight optimization failed: DEN cycle 1 rfree at start of SA cycle: 0.4642 k_rep = 1.00 tardy_tree summary: number of vertices: 16570 number of edges: 16855 find cluster loops: 0 repeats number of fixed vertex lists: 0 number of fixed vertices: 0 number of clusters: 7857 merge clusters with multiple connections: 1 pass number of hinge edges: 7857 number of loop edges: 0 number of loop edge bendings: 0 number of fixed hinges: 0 CAUGHT EXCEPTION: (argument #0) ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0) Traceback (most recent call last): File "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py", line 155, in __call__ result = O.func(arg) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line 227, in try_den_weight_torsion call_back_after_step=False) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py", line 228, in run reduced_geo_manager=reduced_geo_manager) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py", line 86, in __init__ O.weights = target_weights.xyz_weights_result AttributeError: 'NoneType' object has no attribute 'xyz_weights_result' This is a serious error; please contact bugs(a)phenix-online.org. Thanks in advance Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza University of Rome +390649910556

2 6

Fwd: mr_rosetta and Condor
by Dmitry Rodionov 07 Sep '12

07 Sep '12

re: > Submitting job(s) > ERROR: No such directory: /Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1/"/Volumes/condor/Sht1/MR_ROSETTA_5/GROUP_OF_PLACE_MODEL_1" 1)It appears that the submission problem comes from the Condor job description file: Universe = vanilla Error = err.log Output = out.log Requirements = Memory > 256 copy_to_spool = False Initialdir = "/Volumes/condor/Och1/MR_ROSETTA_32/GROUP_OF_PLACE_MODEL_1" Executable = "/Volumes/condor/Och1/MR_ROSETTA_32/GROUP_OF_PLACE_MODEL_1/RUN_FILE_10.sh" Queue I am able to submit the job manually if i remove the double quotes from initialdir and executable lines. Sounds like a very simple problem. Does anyone know how can this be fixed? 2) shortly after submission, the modified (no quotes) job stops with the following: RUN_FILE_1.log: Rebuilding the model /Volumes/condor/Och1/MR_ROSETTA_32/WORK_1/global_1/2vk9_1_chain.pdb with rosetta ================================================================================ Splitting generation of rebuilt models into 1000 jobs with 1 structures generated per job ================================================================================ ******************* ERROR ENDING *************** 'NoneType' object has no attribute 'endswith' ******************* ERROR ENDING *************** Oddly enough, if I run the script locally it runs without this problem. I understand that the error is Python. Does anybody know where it might be coming from? 2)Another thing is that Condor's err.log and out.log are created in the same location and under the same name for all jobs which "may lead to bizarre behaviour" according to the Condor's manual. Might not be a bad idea to name the files something like run_xx_err.log or stick them into the RUN_xx folder for the sake of safety. Thanks! Dmitry

1 0

restraining covalent links between symmetry related molecules
by Dave Lodowski 06 Sep '12

06 Sep '12

Dear all, I am attempting to add a bond restraint that connects a serine in one molecule to a carbon located in its symmetry mate in the adjacent unit cell. Atom selection 1: chain 'A' and resid ' 230 ' and name ' C ' and altloc 'A' Atom selection 2: chain 'A' and resid ' 179 ' and name ' OG ' and altloc 'A' and (*insert symmetry keyword here*) 'x-1,y,z' (altloc B in both cases is not covalently attached) I cannot seem to find a complete description of the atom selection syntax in the Phenix documentation to specify which symmetry mate. and the gui/ phenix graphics does not have any way to generate symmetry mates. What is the keyword that specifies a symmetry mate? Thanks, Dave Lodowski

2 1

Autosol: MIRAS
by ash.k＠aol.com 06 Sep '12

06 Sep '12

Hi all, I am tryingto solve a structure through experimental phasing using AUTOSOL. I have acouple of heavy atom derivative datasets (Hg, La, Eu, Cd) and also a SeMetdata. Unfortunately all the datasets are of low resolution (3.7-4.2A) and thereare possibly 4-8 molecules in the asu. MIR, SAD and MAD alone did not give any convincing solution. However,MIRAS, with a combination of few heavy atom datasets and the anomalous datafrom SeMet crystals, gave a somewhat satisfactory map. But the heavy atom sitepicked by AUTOSOL list only one of the heavy atoms i.e. Lanthanum. In another set of run, the solution of which was not convincing, the heavy atom substructure had only Hg. There are 6Met out of 200 residues in one molecule and mass spec results show that Seincorporation is 100%. Now, mydoubt is that why does the heavy atom substructure contain only La and how canI get the substructure involving Se from this solution (or the datasets used)? Se location is going to help me a lot forfinding a starting point to assign side chains. Anysuggestion would be greatly appreciated. Thanks AK

4 8

Partially occupied side chains in special position
by Nicholas Keep 06 Sep '12

06 Sep '12

I have an ARG which has nice density for its guanadinium group on a 2 fold. This is the same conformer from the two copies. The occupancy of this chain is set to 0.5 and a second conformer that does not cross the two fold is provided. There is clearly a repulsion term in phenix refines that moves the quanadinium away from the two fold. Do the atoms of the guanadinum group need to have an occupancy of 0.25? Can I specify no repulsion between these symmetry elements? Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep(a)mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door

2 1

Adding H atoms - AssertionError
by Kristof Van Hecke 06 Sep '12

06 Sep '12

Dear, When I try to add H-atoms to a metal-coordination complex (not a protein, nor DNA) during refinement or via the ReadySet module, I get the following error: (I have a proper restraints .cif file and without the 'add H-atoms' option during refinement, things work fine,. ) ---------------- AssertionError : Traceback: File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/ cctbx_project/libtbx/thread_utils.py", line 233, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/ cctbx_project/libtbx/runtime_utils.py", line 80, in __call__ result = self.target() File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/phenix/ wxGUI2/SimpleApp.py", line 17, in __call__ return self.target(args=list(self.args)) File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/elbow/ elbow/command_line/ready_set.py", line 1038, in run no_file_access=True, File "/Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/elbow/ elbow/command_line/join_cif_files.py", line 151, in run assert 0 ----------------- I have the latest version of Phenix (1.8.1069) and run it on a Mac Book pro (Leopard 10.5.8). Any suggestions please..? Thank you very much Kristof Van Hecke

5 6

phenix.mr_model_preparation_1.8-1069 can't parse hhr
by Dmitry Rodionov 06 Sep '12

06 Sep '12

Dear all, I was trying to run MR_rosetta, but encountered a problem: my hhr files can't be parsed. GUI does not recognize files as HHR and phenix.mr_model_preparation_1.8-1069 exits with the error below. I can't figure out what does it want from me. Any help will be greatly appreciated. Best regards, Dmitry Reading homology search file: local.hhr Sorry: Uninterpretable: 'Q ss_pred CC-CCCeEEEEECCCCcccccCHHHHHHHHHHHHHhCCCcEEEEechHHH------------------------------\nQ Sht1-d52 42 AP-IPQRVWQTWKVGADDKNFPSSFRTYQKTWSGSYSPDYQYSLISDDSI------------------------------ 90 (428)\nQ Consensus 42 ~~-IPk~IwQtW~~~~~~~~lP~~~~~~i~sW~~~~nP~~~~~l~~D~~~------------------------------ 90 (428)\n .+ |||+||.+|.++ .+|+..+.|+.+| ++.+|||++.+|+|.++ \nT Consensus 93 ~~~IPKiIHyIWiGg----~~P~~~~~yI~sW-kk~~PDYei~lW~Dsna~lA~~LKk~i~e~A~~~~~~~~~~~~~d~~ 167 (551)\nT 2vk9_A 93 STIASKNLSFIWIGG----PISDQSLEYYNMW-KMFNKDYNIRLFYDKNSLLVNTLKTAIIQESSKVIIEQNQSNILDGT 167 (551)\nT ss_dssp SCBCCSEEEEECCSS----CCCHHHHHHHHHH-HHHCTTSEEEEEECTTCCCHHHHHHHHHHHHHHHHHHTTSGGGTTTS\nT ss_pred CCCCCcceEEEEcCC----CCCHHHHHHHHHH-HHHCcCCEEEEEeccchHHHHHHHHHHHHHHHHHHHHHHhhccCccc\n\n\nQ ss_pred --------------------------------------HHHHHHhcccChHHHHHHHh----------------------\nQ Sht1-d52 91 --------------------------------------IPFLENLYAPVPIVIQAFKL---------------------- 110 (428)\nQ Consensus 91 --------------------------------------~~~V~~~~~~~Pdv~eay~~---------------------- 110 (428)\n .+|+...++...+.++.|.. \nT Consensus 168 ~~~~~fy~~~l~~i~~~Q~~f~Nyy~~~~~~~s~D~~ri~yL~~~~~~d~eeLe~~k~~n~~ki~~~~g~DIr~l~~f~~ 247 (551)\nT 2vk9_A 168 YGHNKFYSDRMKLIYRYKRELKMLYENMKQNNSVDDIIINFLSNYFKYDIGKLNNQKENNNNKMIAIGATDINTENILTN 247 (551)\nT ss_dssp CCSCTHHHHHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHTCEEGGGTTCSCH\nT ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcCCCchhHHHhhh\n\n\nQ ss_pred -----------cC-chHHHHHHHHHHHHHHcCCEEEecCceee--ccHHHhhccchh-----------------------\nQ Sht1-d52 111 -----------MP-GNILKADFLRYLLLFARGGIYSDMDTMLL--KPIDSWPSQNKS----------------------- 153 (428)\nQ Consensus 111 -----------lp-~~i~kAD~lRyllL~~~GGIY~DiDt~~l--kPi~~wi~~~~~----------------------- 153 (428)\n ++ +.+..||++|+.+|+.+||||+|+|++|- ..+-.-|..... \nT Consensus 248 ~~~~~Y~~e~~~r~N~aaASDi~R~~il~~~GGiY~D~D~lP~~s~~v~k~I~~~~~~~~~~~e~~~Le~I~k~~~li~~ 327 (551)\nT 2vk9_A 248 KLKSYYYQELIQTNNLAAASDILRIAILKKYGGVYCDLDFLPGVNLSLFNDISKPNGMDSNYWEAAIFEAIANEKKLMNN 327 (551)\nT ss_dssp HHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHCEEEECTTCBSCBCGGGGGGSCCCTTCCHHHHHHHHHHHHHHHTTCCSS\nT ss_pred hHHHHHHHHHHhccchHHHHHHHHHHHHHHhCCEEEeccccccccHHHHHHhcCCCcchhhHHHHhHHHHHHHhHhhccC\n\n\nQ ss_pred ----------------------------hhhcccccccccccccccccccccccccCCCceEEEeecCC---Cccccccc\nQ Sht1-d52 154 ----------------------------WLNNIIDLNKPIPYKNSKPSLLSSDEISHQPGLVIGIEADP---DRDDWSEW 202 (428)\nQ Consensus 154 ----------------------------~l~~~~d~~~p~~y~~~~~~~~s~~~~~~~~~lvvGiE~D~---~~~~W~~~ 202 (428)\n .|. +.+-.+-.+..+ -.. |..+\nT Consensus 328 ~~s~~~d~L~~e~k~~L~~i~~~~~~~~iF~--------------------------pl~d~~Vrd~~~il~R~~-~~~G 380 (551)\nT 2vk9_A 328 YPYKYMEQVPSEIKERILSFVRNHDINDLIL--------------------------PLGDIKISQLEILLSRLK-AATG 380 (551)\nT ss_dssp CCCSSSSSSCHHHHHHHHHHHHTSCHHHHBC--------------------------CCCCCBCCTTCCEEEEEE-CTTS\nT ss_pred CcchhhccCCHHHHHHHHHHHhhccchhhcc--------------------------CccccccCchHHHHHHHH-Hhcc\n\n\nQ ss_pred ccccceEEEEEEEecCCCHHHHHHHHHHHHHHHhhhhhccccccccccccccccccccccccccc-----------cccc\nQ Sht1-d52 203 YARRIQFCQWTIQAKPGHPILRELILNITATTLASVQNPGVPVSEMIDPRFEEDYNVNYRHKRRH-----------DETY 271 (428)\nQ Consensus 203 ~~r~~qf~qw~iaA~PgHPvL~~~I~~I~~~~~~~~~~~~~~~~~~~d~~~~~~~n~~~~~~~~~-----------~~~~ 271 (428)\n | +.+.|.+|+|.+|++++..+|..+..+ |+--++. +..|\nT Consensus 381 w---~~~~N~~m~shkgS~~v~~VI~~~~~~---------------------------Y~~l~~~~r~~v~~~~t~~~~f 430 (551)\nT 2vk9_A 381 K---KTFSNAFIISNNDSLTLNNLISQLENR---------------------------YEILNSIIQEKFKICETYDSYI 430 (551)\nT ss_dssp C---EEEEEEEEEECTTCHHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHHCSSHHHHH\nT ss_pred c---cchhhhhHhhCCCCHHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHhhccccHHH\n\n\nQ ss_pred c-------------------------cchhhccccccCCCcccccCcHHHHHHHHHHH\nQ Sht1-d52 272 K-------------------------HSELKNNKNVDGSDIMNWTGPGIFSDIIFEYM 304 (428)\nQ Consensus 272 ~-------------------------~~~~~~~~~~~~~dv~~~TGP~~~Tdai~~yL 304 (428)\n . .+-.+..-..+....+.+|||++++++..++|\nT Consensus 431 ~s~~~~~~e~~~~~~~~~~~~f~~~i~~Y~~Dg~~pe~~~Ti~LtGP~~~~~~~~dl~ 488 (551)\nT 2vk9_A 431 NSVSELVLETTPKNLSMDGSSFYQQIIGYLSSGFKPEVNSTVFFSGPNIYSSATCDTY 488 (551)\nT ss_dssp HHHHHHHHHHSCSSCCHHHHHHHTTGGGSTTBTTBTTCCGGGTTTSHHHHHHHHHHHH\nT ss_pred HhhHHHHHHhccccccccchhHHHHHHHHhhccccccceeeeeccCcHHHHHHHHHHH'

2 3

mr_rosetta and Condor
by Dmitry Rodionov 06 Sep '12

06 Sep '12

Good day! I am trying to get a bunch of OS X 10.6 workstations managed by Condor to work together on an mr_rosetta project. I am new to batch systems and rather confused. The Phenix manual states: "Single file system required for mr_rosetta All files are stored on a single file system that must be accessible to all jobs." What exactly has to go on the network share and how would I make the execution nodes aware of it? Could somebody please share some information on a working setup of this sort? Thanks! Best regards, Dmitry

2 3

phenix/ccp4 monomer library compatibility
by Wulf Blankenfeldt 05 Sep '12

05 Sep '12

Dear all: this may have been asked a thousand times, but: are the ccp4 standard monomer libraries incompatible with phenix.refine, and if yes, is there an easy way to resolve this? I am refining a structure with an FMN, which I build with the "get monomer" option in coot. Unfortunately, phenix.refine doesn't like it and throws it out. Using a cif generated with elbow, on the other hand, has chirality errors (which I can fix...) and isn't liked by coot (0.6.2), which refuses to refine the ligand. Thanks in advance for your help, Wulf -- Prof. Dr. Wulf Blankenfeldt NW-I, 2.0.U1.09 Universitaet Bayreuth fon: +49-(0)921-55-2427 Lehrstuhl fuer Biochemie fax: +49-(0)921-55-2432 Universitaetsstrasse 30 e-mail: wulf.blankenfeldt [at] uni-bayreuth.de 95447 Bayreuth web: www.biochemie.uni-bayreuth.de Germany

5 4

B factor refinement in recent versions of phenix
by "Weiergräber, Oliver H." 31 Aug '12

31 Aug '12

Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine. The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A². So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8. I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab. Any ideas what might be causing this and how to revert to the original behavior? Thanks in advance Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app

4 5

Phaser and PTNCS - bug fixed in latest builder for Phenix?
by Rafael Lemos Miguez Counago 29 Aug '12

29 Aug '12

Dear all, I noticed on the Phaserwiki webpage (news section) that there is a bugfix (dated 14th of August/2012) for Phaser as the "Packing test was incorrectly applied to reoriented molecules where there was PTNCS". I had a look in the "changes" file, but could not find if this bugfix is part of the latest Phenix installer (dev-1143) or not. Could anybody clarify this point for me? Thanks a lot. Best wishes, Rafael.

3 3

AsCA 12/CRYSTAL 28 Conference and the Bragg Symposium - Early Bird Registration closes this weekend
by John Bruning 29 Aug '12

29 Aug '12

Dear All, Early bird registrations for the Asian Crystallography Association Conference and the Bragg Symposium close this Saturday. You can register for one or both events. **** ** ** The one-day Bragg Symposium on Thursday the 6th of December may be of particular interest as it will specifically address the scientific and historical aspects associated with the centenary of Lawrence Bragg’s explanation of X-ray diffraction. ** ** To register, visit: **** ** ** http://www.sapmea.asn.au/conventions/crystal2012/index.html Kind regards to read this newsletter in your browser click here <http://www.sapmea.asn.au/conventions/crystal2012/emails/enews_01.html>**** [image: cid:[email protected]]**** AsCA 12/CRYSTAL 28 *Conference Newsletter***** Volume 1, May 2012**** Invitation to attend**** *A Joint Meeting of the Asian Crystallographic Association (AsCA), ** Society of Crystallographers in Australia and New Zealand (SCANZ) and the BRAGG Symposium, * November 2012 marks the centenary of the founding of X-ray crystallography by Lawrence Bragg, a field in which he and his father, William, made pre-eminent contributions that were recognised by the award of the Nobel Prize for Physics in 1915. William was the Elder Professor of Physics at the University of Adelaide from 1886 to 1909 and Lawrence was born and educated in Adelaide.**** To celebrate this important anniversary, the legacy of the Braggs’ discoveries in X-ray crystallography and the insights that they have provided into the structure of matter, a combined scientific meeting of the Asian Crystallography Association and the Society of Crystallographers in Australia and New Zealand is to be held in Adelaide from the 2nd to 5th of December 2012. The Conference will be followed by the Bragg Symposium at the University of Adelaide on the 6th of December 2012 that will explore some of the historical context and personal links to the Braggs' work as well as present some of the broader scientific and social impacts of the Braggs' work. The Conference and Symposium will have a strong line-up of national and international speakers.**** Call for Abstracts**** For more information and online abstract submissions please click here: http://www.sapmea.asn.au/conventions/crystal2012/abstracts.html**** Online Registration:**** For more information on online registration and accommodation bookings please click here: http://www.sapmea.asn.au/conventions/crystal2012/rego.html **** **** Conference Secretariat**** [image: cid:[email protected]]**** *sapmea* Unit 12 202 Glen Osmond Rd Fullarton SA 5063 Phone: (08) 8274 6059 Fax: (08) 8274 6000 crystal2012(a)sapmea.asn.au**** ** ** ** **

1 0

Funky message on phaser MR
by Rafael Lemos Miguez Counago 28 Aug '12

28 Aug '12

Dear all, I am getting this message when running Phaser-MR in Phenix (1.8-1069): "Warning: Resolution of data does not achieve (half) expected LLG target: placement of one/first ensemble will be very difficult" The data scales/merges OK. – 99% complete at 2.2A, Rmerge 8.4%. TNCS is detected by Xtriage and Phaser tries to account for that. Coincidently (?) my molecular replacement solution is not looking very good. Any ideas? Best wishes, Rafael.

3 4

HB_score in Ligand Identification
by Brad C. Bennett 23 Aug '12

23 Aug '12

Hello to all- Where can I find a description of what "HB_score" is and how it is calculated in the Ligand Identification program in Phenix? I'm assuming this is a metric for hydrogen bonding capability/propensity of a fit ligand based on distance and angle to model atoms. I have an output rank list of the top 20 ligand fits, ranked by Z-score. The HB_score is all over the place: low = -0.59, high = 77.96, most are between 0-10. I think I understand the correlation coefficient and Z-score but how does the HB_score fit in with these? I can't find this in the documentation or in the Terwilliger et al. (2007) Acta D reference. Somehow I've "lost" the log file, so maybe the information is in there. Thanks in advance! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

2 1

real space correlation
by Bradley Hintze 22 Aug '12

22 Aug '12

Hey Phenix team, I am trying to get real space correlation measurements for 1eao and ran into a problem. $ phenix.fetch_pdb --mtz 1eao $ phenix.real_space_correlation 1eao.pdb 1eao.mtz Multiple equally suitable arrays of observed xray data found. Possible choices: 1eao.mtz:FOBS,SIGFOBS 1eao.mtz:F(+),SIGF(+),F(-),SIGF(-) Please use .labels to specify an unambiguous substring of the target label. Looking in the options for phenix.real_space_correlation it is unclear how to specify the labels for the reflection file. Any assistance on this would greatly be appreciated. Thanks, Bradley -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry Please help me raise money for my ride to assist children with disabilities! <http://www.ridewithoutlimits.org/site/TR?px=1166331&pg=personal&fr_id=1260&…>

3 5

autosol error
by Nora Cronin 21 Aug '12

21 Aug '12

Running phenix.autosol in input wavelength and f" and f' parameters are rejected as follows: "Guessing wavelength for mad is 1.0 Guessing scattering factors for PT at 1.0 A Removing wavelength_list from Facts as length does not match wavelength_list: [1.0721, 1.0538] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Removing f_prime_list from Facts as length does not match f_prime_list: [-17.31, -15.31] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Removing f_double_prime_list from Facts as length does not match f_double_prime_list: [11.93, 10.5] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Why is this rejection of input happening? what does "length does not match" indicate? Best Nora The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

2 1

Reproducing a run in phenix.hyss
by Jeffrey, Philip D. 19 Aug '12

19 Aug '12

I've got an interesting potential S-SAD solution that crops up rarely in a script I was using to trawl parameter space in phenix.hyss. Since I was not optimistic of the outcome I did not save all output files. Hyss appears to use a random number generator and allows the seed to be specified on the command line, so is there any way to figure out what random number seed it used based on the information written to stdout while the program is running ? Merely running the command again does not trivially recreate the solution and egrep -i 'rand|seed' LOG only pulls out: Nigel Moriarty, Reetal Pai, Randy Read, Jane Richardson, David Richardson, time_log: p1_recycling random_omit: 990 1.49 0 0.00151 time_log: random_omit: 891 0.62 0 0.000696 Cheers Phil Jeffrey Princeton

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phenix.refine crash
by Maxime Cuypers 18 Aug '12

18 Aug '12

> > Hi, > > i am refining a neutron structure and i keep having this error: > > > File > "/usr/local/phenix-dev-1129/build/intel-linux-2.6/../../phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/usr/local/phenix-dev-1129/phenix/phenix/refinement/command_line.py", line > 146, in run > call_back_handler=call_back_handler) > File "/usr/local/phenix-dev-1129/phenix/phenix/refinement/driver.py", > line 1533, in run > ncs_manager = self.ncs_manager) > File > "/usr/local/phenix-dev-1129/phenix/phenix/refinement/strategies.py", line > 1109, in refinement_machine > h_params = h_params) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 212, in __init__ > nproc = nproc) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 315, in __init__ > result = self.try_weight(weight, print_stats=True) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 401, in try_weight > minimized = self.minimize() > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 470, in minimize > self.model.set_refine_individual_adp() > File "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/model.py", line > 1231, in set_refine_individual_adp > iselection = selection_iso.iselection()) > RuntimeError: cctbx Internal Error: > /net/longnose/scratch2/phenix/phenix-dev-1129/cctbx_project/cctbx/xray/scatterer_flags.h(417): > CCTBX_ASSERT(f.use_u_iso()) failure. > > i see the last line is already a known issue as it was already posted in > phenixbb in 2010 but was perhaps solved offline. > > thanks in advance for any help (as i am really stuck) > > -- > Dr. Maxime Cuypers > Institut Laue Langevin (ILL), Deuteration lab > Rue Jules Horowitz, 6, BP 156 > 38042 Grenoble cedex 9 > France > > >

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Real-space and twin refinement
by Haim Rozenberg 13 Aug '12

13 Aug '12

Hello, We've just downloaded and install the new dev-1129 release of phenix hoping to be able to run RS refinement on our twin structures. According to the change log it should be possible with this version. ------------------------------------------------------------------------ Version 1.8.1 and nightly builds (TBA) ====================================== - phenix.refine: - overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior) - improvements to torsion NCS rotamer correction - real-space refinement for twinned structures ------------------------------------------------------------------------ Unfortunately, while trying to run - through the GUI - phenix dev-1129 with our twin setting and the "Real space" option, the usual message popped up: "PHENIX error: Real-space refinement is not available for twinned structures." FYI, it runs just fine without the "Real-space" option. Did we have false hopes? Did we misunderstood? Is that a bug? All the best, Haim ============================================ Haim Rozenberg, PhD. Department of Structural Biology Kimmelman Building Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972-8-9344289 FAX:+972-8-9344136 E-Mail: haim.rozenberg(a)weizmann.ac.il<mailto:[email protected]> ============================================ "Quis custodiet ipsos custodes?" D.I. Iuvenalis

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difficult phasing problem
by Ian Slaymaker 09 Aug '12

09 Aug '12

I am trying to solve the structure of a ~30kd monomeric protein for which we have 2.5A diffraction data, and a search model with ~65 % similarity (i have tried, homology models of this and others, as well as using sculpter to build several variations of core search models). I have tried all my possible space groups and a huge range of parameters, and mr_rosetta to rebuild some of my better (but still bad) MR solutions. My LLG is persistently negative (<-1000), which may be due to translational noncrystallographic symmetry which was identified by xtriage. We have unfortunatly been unable to phase this data with selmet SAD, so I am looking for some other MR things to try. Any suggestions for working with tNCS (if this is really the problem) would be much appreciated.

2 1

test set count question
by Filip YABUKARSKI 08 Aug '12

08 Aug '12

Dear all, I am refining a structure with phenix.refine using a .mtz which contains F/SigF and DF/SigDF (CCP format from xdsconv) and i have something like 10000 unique reflections. The test set was created with the uniqueify script. If I understand correctly in the manual it is written that phenix.refine will separate the <F>/<SigF> into "F(+) SIGF(+) F(-) SIGF(-)), instead of keeping the original non-anomalous amplitudes". My question is about the "FREE R VALUE TEST SET COUNT" in the .pdb after phenix.refine. If I understand correctly the number for the test set will also be "doubled" because the <F> will be separated into F+ F-? Logically both F+/F- after separation are kept in the test set is this right? And an impair number for the test set in this case means that only the F+ OR F- was observed? Sorry if I ask a trivial question but I just want to be sure I am using the program in the right way Thanks in advance Filip

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Re: [phenixbb] test set count question
by Kay Diederichs 08 Aug '12

08 Aug '12

Dear Filip, concerning XDSCONV: if FRIEDEL'S_LAW=FALSE, using filetype of CCP4, you get F,SigF,DF,SigDF,isym using filetype CCP4_F, you get F,SigF,F(+),SigF(+),F(-),SigF(-) using filetype CCP4_I, you get IMEAN,SIGIMEAN,I(+),SIGI(+),I(-),SIGI(-) so you can (and should) directly output from xdsconv what you need for a downstream program. A short explanation is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv Detailed explanation of each format is at http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_formats.h… HTH, Kay

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changing a project directory
by Kendall Nettles 08 Aug '12

08 Aug '12

Dear PHENIX developers, I want to migrate my PHENIX project directories. I moved one project directory as a test, and the GUI doesn't give an opportunity to relocate, which would be a nice feature. Is there a way to edit their location for the PHENIX GUI? Kendall

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two problems about phenix.mr_rosetta
by chen c 08 Aug '12

08 Aug '12

Dear all: I've collected a data set for my crystal, which is a two-protein complex. However, normal molecular replacement method gives no solution and thus didn't work. Right now I'm struglling with the phenix.mr_rosetta method. However, I've got several problems when reviewing it, and thus looking forward to get some advice here. 1: There are such words *"NOTE 2: If your structure contains more than one chain or requires more than one homology model to represent the structure, then you need to use mr_model_preparation and phenix.automr to place your model. Then you can start phenix.mr_rosetta with already_placed=True**"* in phenix documentation page. My understanding for this sentences is: the solution derived from *automr* is treated as an original searching model for phenix.mr_rosetta, in which case, we should add the command line *"run_prerefine=True \ number_of_prerefine_models=1000"*. However, what is *mr_model_preparation * for? And if no solution is given by *automr*, what should I do? What's more important, why not endow the phenix.mr_rosetta program to be capable of dealing with data set from multi-chain protein complexes? Since I thought the idea of preliminary manipulation by the program *automr* would decrease the power of *phenix.mr_rosetta*. 2: Two .hhr files are produced. But as displayed in the phenix.mr_rosetta documentation page, only one .hhr file like *"hhr_files=bfr258e.hhr"* are listed in the command line. Why? Could somebody give me any advice on this, please? Thank you and best regards chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China -

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refining multiple conformations
by Kendall Nettles 08 Aug '12

08 Aug '12

Hi, We have a structure with the ligand showing two overlapping conformers. When we refine it with both conformers separately, it is pretty clear that there are substantial differences in the protein as a result, for about a third of the protein chain. My question is, would it be better to try to define altloc for those specific regions, or would it be OK to refine with two entire alternate protein chains? There is also a second protein chain that shows only a single binding mode for the ligand. It's a 2.0 angstrom structure with 4000 atoms and 27,000 reflections. The yellow map goes with the green model in the attached pic. Also, do we want to let each amino acid have its own occupancy? or should one ligand copy and one chain all have the same occupancy? I'm leaning towards the latter since the differences should be directly tied to the ligand binding mode. Kendall Nettles [cid:[email protected]]

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mr_rosetta problems
by Ian Slaymaker 07 Aug '12

07 Aug '12

I am trying to get mr_rosetta working on our cluster and am running into some problems I am not sure how to solve. The phenix_regression.wizards.test_command_line_rosetta_quick_tests tests went smoothly were completed. However, my first test run with all the defaults (not submitted to multiple processors) using my reflection file, HHR analysis file, sequence file, and the 2 fragment files failed with the below errors. I checked all the files, and it seems this is a problem with the fragment files but I am not sure exactly what they are supposed to look like. I thought it could be because our cluster doesnt have access to any outside networks...is this a problem with rosetta not being able to download pdb files? if so, is there a way to supply them internally? The aligned model looks somewhat what I expected it to (same beta sheet arrangement) but it seems to be incomplete. Any help would be very much appreciated! Splitting work into 100 jobs and running with 1 processors using sh background=None in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 Starting job 1...Log will be: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log ******************* ERROR ENDING *************** mr_rosetta failed... ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log : to match the actual PDB sequence: (protein sequence) New alignment line 4 for PDB: (protein sequence) Start position of target sequence in sequence file: 0 Aligned model for comparison: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/aligned_model.pdb Log for rebuilding: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** Failed to run REBUILD...see log file in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log The rebuild log had repeats of several errors that I am not sure how to address: core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 3 (repeated several times) core.fragments.ConstantLengthFragSet: line too short: Skipping line ' (repeated several times) core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file/dataFiles/aat000_03_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug none 1

4 5

Ordered solvent distances
by Abhinav Kumar 03 Aug '12

03 Aug '12

Hi, The default minimum distance that a water gets placed near protein/water atoms using 'ordered_solvent=true' option in phenix.refine is 1.8. Isn't this too close? Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992

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Lost my job history, can it be recovered? (GUI)
by Andrew Waight 02 Aug '12

02 Aug '12

Hello All, It just so happened that my lab's server ran out of space (someone else uploading datasets) while my phenix rosetta MR job was running. Now the GUI no longer shows any job history in the job history tab (although on the title page the number of jobs is correctly displayed. I cannot find any information on how or if its possible to recover my job history in the GUI. Any tips? Thanks so much. Drew

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July 2012 Computational Crystallography Newsletter
by Nigel Moriarty 31 Jul '12

31 Jul '12

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles ----------- cctbx tools for transparent job execution on clusters On the analysis of residual density distributions on an absolute scale Short communications -------------------------------- DETAC: tools to detect alternative conformations by unrestrained refinement ERRASER, a powerful new system for correcting RNA models Fitting tips - Rotamer correction with backrub -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Hi all, I am starting to use a new computer cluster and just found out by uname that it runs Darwin OS? It is totally new to me and I am wondering if Phenix would run on it? should I use just some Mac installer? I would really appreciate any advices! Thank you! Sincerely, Tanya

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Re: [phenixbb] what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Thank you Miguel and Ben! I did found the newest release at the cluster after I learned how to use "find" properly! In particular, thank you for pointing out the script to source! Best regards, Tanya

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