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Error while updating water
by Subhani Bandara 01 Jul '13

01 Jul '13

Dear all, I am refining a protein structure at 2.5 A. After running some refinements with water update option on, I manually added water to some positions and ran without water update option as it removes those water from the sites and show green density around. Then after some refinements like this, I tried to use water update option to add water to some newly appeared density. When I check the option to update water using dev 1418 version it stops with the following error. Also when not using water update option, refinement statistics got worse when I used 1418 compared to 1.8.2-1309 with refinements using same inputs and options. R work-0.1988 compared to 0.1920 with 1.8.2-1309 Rfree-0.2623 compared to 0.2490 with 1.8.2-1309 Traceback: File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/thread_utils.py", line 236, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 94, in __call__ result = self.target() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 73, in __call__ result = self.run() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 69, in run refine_object = self._run(args, callback) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 85, in _run call_back_handler=callback) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/command_line.py", line 161, in run call_back_handler=call_back_handler) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/driver.py", line 1630, in run ncs_manager = self.ncs_manager).result File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/strategies.py", line 155, in __init__ neutron_refinement2 = self.neutron_refinement2) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 26, in __init__ self.__call__() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 36, in __call__ self.__getattribute__(method_name)() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 106, in run_sol mc = self.macro_cycle) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 79, in _need_to_run else: raise RuntimeError("Not a valid mode: %s"%mode) Thanks in advance for any help Subhani

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automatic weight optimization
by Michael Thompson 30 Jun '13

30 Jun '13

Hello Phenix Folks, I have a few questions about the automatic weight optimization in phenix.refine. I have read the manual, but I feel like maybe I'm missing something. I apologize in advance if these are naive questions, but here goes. I ran phenix.refine with a .def file, in which I set the following parameters: target_weights { optimize_xyz_weight = True optimize_adp_weight = True wxu_scale = 2.72 } My goal was to optimize both xyz and adp weights. In the log file, I see something like this: ===================== xyz refinement (lbfgs minimization) ===================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 21.06 20.38 -0.67 0.033 2.0 6.1 0.0 6.6 0 none 0.154 0.1685 19.79 21.26 1.47 0.012 1.3 7.6 0.0 5.8 0 2.494 0.131 0.0499 Legend: - first line corresponds to starting state (before refinement) - R-factors reported in percent - delta is Rfree-Rwork in percent - CLASH is all-atom Molprobity clashscore - ROTA is percent of side-chain rotamer outliers - RAMA is percent of Ramachandran plot outliers - CBET is number of Cbeta deviations - WEIGHT is relative weight between X-ray (or neutron) target and restraints - TARGETS: the values of X-ray (or neutron) and restraints target functions ================================ ADP refinement =============================== ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 19.79 21.26 1.47 1.909 20.062 0.661 0.131 19.80 21.28 1.49 1.761 20.011 0.007 0.130 19.77 21.41 1.64 1.838 19.884 0.030 0.125 20.30 22.63 2.34 2.369 19.168 0.122 0.111 20.17 22.82 2.64 2.886 18.929 0.243 0.107 20.07 23.04 2.97 3.771 18.737 0.365 0.104 20.04 23.14 3.10 4.106 18.751 0.486 0.103 20.00 23.19 3.19 4.496 18.794 0.608 0.103 19.98 23.23 3.25 4.846 18.851 0.729 0.102 19.97 23.27 3.29 5.115 18.940 0.851 0.102 19.95 23.30 3.36 5.420 18.988 0.972 0.101 19.94 23.33 3.39 5.579 19.008 1.094 0.101 19.93 23.29 3.36 5.598 18.917 1.215 0.101 max suggested <Bi-Bj> for this run: 10.00 max allowed Rfree-Rwork gap: 5.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.007 Accepted refinement result: 19.80 21.28 1.49 1.761 20.011 0.007 0.130 The output kind of makes me feel like the adp weight is being optimized, but the xyz weight might not be. There is a list of statistics for varying values of the adp weight, but there is no similar list in the output from the xyz refinement stages. So my questions are: Is the xyz weight being optimized? Did I miss something in the input that is required to turn on xyz weight optimization? If the weight is indeed being optimized, then I must be misinterpreting the log file. How can I check to make sure the xyz weight optimization is running? Thanks for the help!! Mike Thompson -- 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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Format problem of restraint file
by Xiang Li 30 Jun '13

30 Jun '13

Hi everyone, I generated the basepairing restraint file by command phenix.secondary_structure_restraints MR.1.pdb > ss.eff . Then I opened the ss.eff file with gedit and edit the basepairing information. However, after I finished editing and saved the file, the refine program can not read the file. The error is "This application does not support the file type for ss.eff (format:txt)". I have attached a copy of the eff file. Do I have a way to solve the problem? Thanks for your help! Sincerely, Xiang

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unwanted disulfids and geometry restraints
by Ursula Schulze-Gahmen 30 Jun '13

30 Jun '13

I have 2 questions: 1) I am using phenix.refine on the command line with a .eff file as input that was modified from previous GUI phenix runs. My structure has several Zn atoms and readyset creates a geometry_restraints file for the Zn interactions. I am not sure if phenix.refine gets these restraints when I run it from the command line. Do I need to read this file in some specific way? 2) The other question is: phenix refines several of the Cysteine neighbors in the Zn environment as disulfids, but they are not. How do I prevent this from happening? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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Re: [phenixbb] what about heavy atom as model for MR
by zhaoy 29 Jun '13

29 Jun '13

Hi, It's my pleasure to recieved so much wonderful advice and I am trying according to the suggestions. I have used phenix.explore_metric_symmetry to see if there is any relationship between tetragonal and orthorhombic lattices. But the result suggests there is no relationship. In addition, I have some questions about the molecular replacement when density map entered as model. How to define clash between the model and How the value of RMS error of the density model impact the final MR result? Thank you! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China Randy Read 写: Sorry, I'm coming a bit late to this thread, and most things I would have suggested have already been covered by Tom and Paul. Certainly there are examples in the literature of people using MR to place a heavy atom substructure against the anomalous differences, but as Tom pointed out there's the complication of making sure that you get the Se sites from one molecule and not from a combination of symmetry-related molecules, which probably won't have the same relative arrangement in the other crystal form. The one remaining thing I'd like to explore is whether you're sure that you've carried out the molecular replacement with density properly. This has become easier (with Tom's phenix.cut_out_density program), but it's still relatively complicated and error-prone. First, you have to be sure that you've cut out the density essentially for one molecule, and not a mixture of symmetry-related molecules. If the location and rough shape of the molecule isn't clear in your map, you may have to try things like cutting out spheres of density from different places in the unit cell and seeing which gives the clearest MR solution. Second, you have to make sure that you place the density in a reasonably large unit cell, 2.5-4 times the extent of the density that you've cut out, before using it as an MR model. Third, you have to choose an appropriate value for the effective RMS error of the density model. If your phases go to 4A, then a number like 1.5A to 2A might be appropriate. In our tests, the map can be pretty noisy but you can still get a very clear signal from the MR search. Of course, if the phase information is very weak, it still may not work even with an optimal envelope. Best wishes, Randy Read On 23 Jun 2013, at 15:56, "Terwilliger, Thomas C" <terwilliger(a)lanl.gov> wrote: You could try both the isomorphous and the anomalous differences. Each one has some useful information. You can even combine them but I'm guessing it won't help too much. Paul Adams' suggestion to check out related space groups is a very good one. Phenix.autosol only tries the opposite hand, so you have to try all the different screw axis possibilities that are not related by inversion. Another thing you could try is to repeat your MR with density from your map ( against the 2.6 A native) and get a long list of solutions. For each solution take the phases after MR and use them to calculate an anomalous difference Fourier for your semet P2221 data. Then notice if there are peaks in this map, and whether these peaks have the same relationship to the MR-placed density as you saw in your original map. If yes, you may have a solution. All the best, Tom T From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of zhaoy [zhaoy(a)moon.ibp.ac.cn] Sent: Sunday, June 23, 2013 3:32 PM To: PHENIX user mailing list Subject: Re: [phenixbb] what about heavy atom as model for MR Thank you very much. I will try as you said. The P2221 dataset's qulity are not very well. The points from diffraction image are not sharp. Besides, native dataset is 2.6A, setmet anomalous datasets is only 4A. So I have not obtained the solution with p2221datasets. There is only one molecular per AUS at p4322. So, from the initial map, I can confirm the heavy atom sites from the same molecular. Maybe I have a general idea about the method you said. But I still puzzled which F difference should I use, isomorphous or anomalous differences? Thanks! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China Terwilliger, Thomas C 写: I'm not sure if there is a tool that will create the file you want for this. You could however just write a little script that reads in a .sca file and calculates F from I, subtract F+ - F- to get Dano, square that, write out Dano** 2 and sigma(Dano**2) as another .sca file. Then you could use this as input to molecular replacement with your sites from the P4322 dataset. There is an important caveat to this approach however: your sites from the P4322 have to be all part of the same molecule, and this might or might not happen automatically. If some sites are from one molecule and others from another molecule, then in the other crystal form their relationship won't be correct. If there is only one molecule in the au then this might or might not be a big problem. If there are more than one it is very likely to be a big problem. This would apply to the density search that you carried out as well. If your density is good enough to see where the molecule is, you might be able to figure out which of the symmetry-related sites to include in your MR search. Nevertheless as this is easy it seems like a fine thing to do. However I am wondering if it will work because your 2.6 A semet anomalous dataset did not yield a solution by itself, which is a little surprising... Also of course if your P4322 solution is not actually right or even just not close enough it would not work. -Tom T From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of 赵岩 [zhaoy(a)moon.ibp.ac.cn] Sent: Sunday, June 23, 2013 7:52 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] what about heavy atom as model for MR Hi everyone, The heavy atoms(Se-Met) were located at P4322 space group(4A). But the initial density map is so bad that I can not build the initial model. Meanwhile, I have another two datasets, native(2.6A) and se-met anomalous dataset with space group P2221. But these two datasets have no solution. I have tried the initial map from sp P4322 as a model to do molecular replacement. But no MR solution. So, I want to know how can I use the heavy atom as model to do MR with isomorphous or anomalous differences? Thanks! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Is DEN refinement working?
by Wallen, Jamie 28 Jun '13

28 Jun '13

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PHASER-TFZ scores with ensembles higher?
by Jan Gebauer 28 Jun '13

28 Jun '13

Dear Phaser users, I recently tried to solve two difficult MR jobs by using ensembles in PHASER. With ENSEMBLES in this case I mean aligned structures prepared for PHASER by Phenix.ENSEMBLER. In both case I got solution with rather high TFZ-score (> 8), which I couldn't get wit individual structure, but was not able to refine them. My question is, whether using ensembles would increase the Z-Score without really improving phases. In other words, if there is another cut-off for the "Phaser solved it" Z-score, when using ensemble in contrast to single structures... Regards, Jan -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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refining the anomalous Se in MSE using Phenix Gui
by Kenneth A. Satyshur 27 Jun '13

27 Jun '13

Sirs: I am trying to refine the anomalous data in phenix refine. I am using the GUI and I get a box for the anomalous groups. But I when I put in 'Se' and refine: phenix says 'Sorry'. If I use View, I get all atoms in a viewer. I have 5 molecules of 330 residues each and 25 total Se atoms. I cannot possibly pick them out from the molecular display. Then I tried to make a heavy atom file with just selenium in it, but on input, it is read as a 'input model' and when I refine, it says 'duplicate atoms'. Without the anomalous refine, there is a lot of residual Fo-Fc density around the seleniums in the maps. How do I enter the 'anomalous group' into phenix refine. What is the syntax? I can find no help file or documentation on this. Anyone done this before? thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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Phenix version 1.8.2 released
by Paul Adams 26 Jun '13

26 Jun '13

The Phenix developers are pleased to announce that version 1.8.2 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/ Highlights from this version: Ensemble refinement, updated hydrogen parameters in refinement and validation, mmCIF reading and writing, LLG maps output from refinement, ligand pipeline for automated solution of protein/ligand complexes, autobuilding starting from a very accurate but very small part of a model, CC* calculation from unmerged data, maximum entropy maps, and PDB editor. Graphical interface: ==================== - New GUIs: phenix.merging_statistics, phenix.pdb_editor General: ======== - Multiple bug fixes - phenix.refine, phenix.reduce, and MolProbity updated to use consistent, revised, electron-cloud centers for hydrogen positions as default (for X-ray) - also see MolProbity website for details: http://molprobity.biochem.duke.edu - mmCIF format now supported in place of PDB format for input to many programs - new commands: phenix.ensemble_refinement, phenix.ligand_pipeline, phenix.sort_hetatms, phenix.cc_star, phenix.pdb_editor, phenix.maximum_entropy_map Refinement: =========== - phenix.refine - support for LLG map type - uses Phaser to compute residual anomalous LLG map - best when used with group_anomalous strategy, which will flatten the LLG map around existing anomalous scatterers with refined f'/f''. - alternatively, anomalous_residual map type (similar but less sensitive) - automatic linking in refinement and pdbtools for residues in the same chain - enabled with automatic_linking.intra_chain=True; this includes carbohydrate linking to protein and between sugars, and covalently bound ligands. - optional output of mmCIF format model and data files - phenix.ensemble_refinement (new command): - New method for refining ensemble models - Combines MD simulation with X-ray restraints that simultaneously account for anisotopic and anharmonic atomic distributions. - For full description see: Burnley BT, Afonine PV, Adams PD, Gros P. 2012. Modelling dynamics in protein crystal structures by ensemble refinement. eLife 1:e00311. doi: 10.7554/elife.00311. Experimental Phasing and Model Building: ======================================== - phenix.autobuild: - now uses torsion NCS parameterization when NCS is used in refinement - building starting from a very accurate but very small part of a model: You can now use the keyword rebuild_from_fragments=True to start rebuilding from fragments of a model. You might want to use this if you look for ideal helices using Phaser, then rebuild the resulting partial model, as in the Arcimboldo procedure. The special feature of finding helices is that they can be very accurately placed in some cases. This really helps the subsequent rebuilding. If you have enough computer time, then run it several or even many times with different values of i_ran_seed. Each time you'll get a slightly different result. - Base-pairing in RNA building -- phenix.autobuild will now try to guess which bases in a model are base-paired, and if there is no positive sequence match to the model, the bases that are base-paired will be chosen to be complementary. You can set the cutoff for base pairing with the keyword dist_cut_base. - waters are automatically named with the chain of the closest macromolecule if you set sort_hetatms=True. This is for the final model only. - you can supply a target position for your model with map_to_object=my_target.pdb. Then at the very end of the run your molecule will be placed as close to this as possible. The center of mass of the autobuild model will be superimposed on the center of mass of my_target.pdb using space group symmetry, taking any match closer than 15 A within 3 unit cells of the original position. The new file will be overall_best_mapped.pdb. Molecular Replacement: ====================== - phenix.mr_rosetta - You can now give commands for Rosetta in mr_rosetta, including a command to specify where disulfide bonds are located - The Rosetta models are now identified by an ID number so that they have unique names - Default number of homology models to download is now 1 (was 5) - Default number of NCS copies (if ncs_copies=Auto) is number leading to solvent content closest to 50%; if ncs_copies=None then all plausible values of ncs_copies are tested. New commands: ============= - phenix.ligand_pipeline (new command): - combines Xtriage, Phaser, eLBOW, phenix.refine, AutoBuild, and LigandFit to automatically solve protein/ligand complexes - optional integration with Coot (parameter interactive=True) allows semi-interactive operation where more rebuilding is required - phenix.cc_star (new command): - combined assessment of model and data quality, as outlined in Karplus & Diederichs (2012) Science 336:1030-3. - summary also output by phenix.model_vs_data if additional unmerged_data keyword is specified - phenix.maximum_entropy_map (new command): - tool to compute maximum entropy map from map coefficients. The program reads input Fourier map coefficients and modifies corresponding synthesis using Maximum-Entropy Method (MEM). The MEM modified map is everywhere positive, smooth and is of higher resolution. The method uses is a modification of Gull & Daniell (1978) algorithm. - phenix.sort_hetatms (new command): - rearranges heteroatoms (ligands, waters, etc.) in a model so they are paired with the nearest macromolecule chain, similar to the PDB's processing of models - phenix.pdb_editor (new command): - graphical editor for PDB files, based on tree view of model hierarchy - perform common operations such as chain renaming, renumbering, manipulation of atomic properties, add/remove atoms Ligands: ======== - phenix.ready_set: - methyl rotations now automatic when adding explicit hydrogens (also in phenix.reduce) - more options adding deuteriums to a model have been introduced Miscellaneous: ============== - phenix.xtriage: - include merging statistics if unmerged intensities are used as input - phenix.maps: - added wavelength parameter and support for anomalous residual and Phaser LLG map coefficients 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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what about heavy atom as model for MR
by 赵岩 26 Jun '13

26 Jun '13

Hi everyone, The heavy atoms(Se-Met) were located at P4322 space group(4A). But the initial density map is so bad that I can not build the initial model. Meanwhile, I have another two datasets, native(2.6A) and se-met anomalous dataset with space group P2221. But these two datasets have no solution. I have tried the initial map from sp P4322 as a model to do molecular replacement. But no MR solution. So, I want to know how can I use the heavy atom as model to do MR with isomorphous or anomalous differences? Thanks! -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China

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