- phenixbb - phenix-online.org

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 27 Sep '12

27 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

2 5

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

2 2

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

3 2

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 21 Sep '12

21 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

2 1

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

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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

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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

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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

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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

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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

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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'

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