- phenixbb - phenix-online.org

phenix.rosetta_refine
by Guenter Fritz 15 Oct '13

15 Oct '13

Dear Phenix developers, I am working on a 3.6 A structure and want to try the latest joint development of phenix and rosetta. Is there are kind of "how_to" available online? Some do's and don'ts? Best, Guenter

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Phenix on Ubuntu12.3
by Swastik Phulera 12 Oct '13

12 Oct '13

Dear All, I am setting up a computer with ubuntu(12.3) installed on it. running "uname -rm" gives me 3.8.0-31-generic x86_64. I am trying to install phenix on this machine, as recommended I downloaded the 64 bit kernel 2.3 (64bit fedora 3 ) command line installer. I then ran ./install and source the required file by: source /usr/local/phenix-1.8.4-1496/phenix_env.sh but some how phenix refuses to start, following is the error phenix Traceback (most recent call last): File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 22, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 16, in run from wxGUI2 import App File "/usr/local/phenix-1.8.4-1496/phenix/wxGUI2/App.py", line 15, in <module> import wx File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory Any suggestions would be welcome. regards Swastik

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Re: [phenixbb] Problem in reducing R-factor
by Nathaniel Echols 12 Oct '13

12 Oct '13

On Fri, Oct 11, 2013 at 6:19 PM, Ryan Spencer <rspencer(a)uci.edu> wrote: > For high resolution structures, below 1.5 Å, is there a set of > rules > for best practices for refinement? > Not really rules that I'm aware of... just general guidelines, and not well-codified. I've wanted for a long time for us to write some sort of extensive how-to across all resolution ranges, but like everything else, this has to compete with writing code and "real" papers. As Pavel mentioned, these resolution limits are somewhat subjective depending on completeness, how aggressively you process the data, etc. But, a few basic suggestions: - you will probably not want to use real-space refinement after the first couple of rounds - start parameterizing conservatively, then get more aggressive as you near the end of refinement (if nothing else, it's faster this way) - don't use any restraints other than the default geometry restraints plus whatever custom bonds are required by the chemistry (e.g. prosthetic groups) - use hydrogens by the end of refinement, but riding only until you're at subatomic resolution - the automatic weighting is probably going to work great; weight optimization might help for the final round, but probably not necessary - below 1.5Å, try making non-water/non-hydrogen anisotropic (and compare to purely isotropic); below 1.2Å, you can start thinking about making all non-H/D anisotropic. (Also note that heavier atoms can become anisotropic even earlier, so in your case, refining individual anisotropic B-factors for iodine and TLS for everything else would be a reasonable alternative.) - you should probably be able to get rid of all geometry outliers, including clashes - but you may see real (correct) Ramachandran or rotamer outliers at this point - you're inevitably going to see more blobs in the difference map that you can't explain than usual. don't sweat it. - you should definitely see a fair number of alternate conformations - I don't know what is expected statistically but I'd say at least 10% of protein residues will have them - pay attention to waters with close contacts to oxygen - these may be sodium (or other) ions I've attached a few slides that give *very approximate* suggestions - basically just reframing what Pavel and others have said over the years. Although some of these are pretty clear-cut (e.g. you absolutely do not want to use a reference model), you will always need to experiment somewhat to find out what is best for *your* model and data. I think based on your R-factors and statistics that you're headed in the right direction. I'd try to get the clashscore as close to zero as possible, though. I've been toying with different parameters and found that the > weighting didn't make a huge difference, which is probably expected, with a > 1.3 Å dataset. Do stereochemical/ADP weights have any effect? > Do you mean weight optimization? I wouldn't expect it to make much difference. > For the particular data set I'm working with, I'm refining directly > against anomalous data, more specifically against 12 Iodines. Refining the > f' and f" has worked well, generating a beautiful density map. > Good idea. Also consider looking at the anomalous residual map (map_type=anom_residual), which may show weaker anomalous scatterers like chloride or sulfur. (It will be flattened around the iodines if you refine their f'' values.) Refining against the model with hydrogens increased the Rfree/Rwork > values by about 2 points. From what I've read previously I thought refining > hydrogens in a non-"riding" model was only valid below ~1.0 Å. > I'm not sure what you mean here. Did you use the riding model and it increased R-free? Or only when you let them refine individually? The default is now to switch to individual only at 0.9Å or less. > by a few points. For water, I assume that at this resolution there is a > combination of anisotropic (big banana looking density) and isotropic > waters > and that one cannot simply rely entirely on the water_update option. > Yes, at some point you will need to complete the waters yourself. Those bananas may not be simply anisotropic waters, but split sites. You may see other small ligands too. The twin law has worked great, usually dropping Rfree/Rwork values > by 5 points or so. > Just remember to be careful when interpreting the effect of twin law application - I think in this case it's probably quite reasonable, but at lower resolution and with a worse model it can be extremely deceptive. I apologize if any of this is common knowledge and shows my relative > inexperience when it comes to best practices for crystal refinement. > No need to apologize - it is all oral tradition anyways. It is much better to ask questions now than to do something blindly and regret it later. -Nat

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Problem in reducing R-factor
by Singh, Bishal 12 Oct '13

12 Oct '13

Hi all, I am solving a crystal structure at 1.3Å. Completeness of the data-set and Figure of merit at this resolution are 99.5% and 0.62 respectively. Structure has two molecules per asymmetric unit. I used TLS parameters and NCS restraints. WXC_scale and WXU_scale are 0.50 and 1.0 respectively. Rwork and Rfree are 18.09 and 19.62 respectively. I tried with reducing WXC_scale and WXU scale to 0.25 and 0.30 respectively but it did not help. Please suggest me if I need to change some parameters. I shall be grateful for your help. Thanking you, Bishal Singh Graduate student University of Heidelberg, Germany

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special positions Refinement crash
by Yarrow Madrona 11 Oct '13

11 Oct '13

Hello, I am trying to do a refinement and I get an error that I think means I have atoms on special positions. The refinement stops and gives the following output given below. Any help would be appreciated. I am not sure how to exactly determine which atoms are at special positions. Thank you. -Yarrow |-real space refinement (target=simple)---------------------------------------| | start: r_work=0.5500 r_free=0.5441 rmsd: bonds=0.019 angles= 1.68 weight= 50| | final: r_work=0.5309 r_free=0.5358 rmsd: bonds=0.029 angles= 2.45 weight= 80| | --------------------------------------------------------------------------- | ==================== Compute data/restraints target weights =================== Traceback (most recent call last): File "/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py", line 159, in run call_back_handler=call_back_handler) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1593, in run reference_model_manager = self.reference_model_manager).result File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py", line 171, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 87, in __init__ self.call(self.weight, "Compute data/restraints target weights") File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 137, in call func(prefix = prefix) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 302, in weight log = self.log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py", line 20, in run log = log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 368, in __init__ self.xyz_weights_result = self.xyz_weights() File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 411, in xyz_weights log=self.log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 294, in __init__ verbose=0) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py", line 29, in shake_sites max_iterations = max_iterations)) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 43, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py", line 259, in run log) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py", line 127, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 89, in compute_functional_and_gradients self.apply_shifts() File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 70, in apply_shifts site_cart=self.tmp.sites_shifted[i_seq]) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py", line 609, in correct_special_position raise AssertionError(error_message) AssertionError: Excessive special position correction: unit_cell: (56.278, 67.256, 106.26, 90, 90, 90) space_group_info: P 21 2 2 special_op: 1/2,y,1/2 site_frac: (0.5090941495765681, 0.42722892547242985, 0.5083083194012079) site_special_frac: (0.5, 0.42722892547242985, 0.5) distance_moved: 1.02047 Phenix v. 1.8.4-1496 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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r-free output by resolution shell
by Ursula Schulze-Gahmen 11 Oct '13

11 Oct '13

Where can I find an output of Rfree in resolution shells? I ran phenix.model_vs_data and I don't see it there. I also didn't find it in the log-files of refinement. Maybe I am just overlooking it. Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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Project Database Location
by David Shin 10 Oct '13

10 Oct '13

Hi - I had a computer disk go down and want/need to migrate files over manually. I just reinstalled a 1.8.3 version of phenix from a disk image onto OS X 10.6.8. Upon launch, it appears it cannot find my old project database. I was wondering if this is something that can relatively easily migrated over from my backup disk, and where it lives. Thanks, Dave -- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA

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Worse R factor with newer version of phenix
by Jan van Agthoven 09 Oct '13

09 Oct '13

Hi everyone, I've been working on a low resolution structure (3.6A) which was previously refined with phenix 1.8_1069 (with a reference model, strategy=individual_sites,individual_adp ). I used the same input files and parameters and ended up with significantly different R factors. Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059 Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997 For the old version and Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141 Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737 with the new version 1.8.4 Remarkably it also came with an increased number of C-beta deviation (0 against 16!). Adding tls refinement or ramachandran restrains did not help. Now because I was using the .eff file of an old version of phenix, it came with a long list of unused parameters. These parameters however were all used by default. What should I do? Should I go back to this old phenix, or is there a way to improve the result? Thanks,

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Phenix version 1.8.4 released
by Paul Adams 09 Oct '13

09 Oct '13

The Phenix developers are pleased to announce that version 1.8.4 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: Automated MR/ligand fitting/refinement pipeline (phenix.ligand_pipeline), improved determination of bulk solvent masks, improved real space refinement, GUI for ERRASER, improvements to AutoSol and AutoBuild, improvements to Phaser, improvements to Guided Ligand Replacement, 64-bit Windows 7 installer. Graphical interface: ==================== - New GUIs: ERRASER, phenix.dynamics - Pause/resume function for most programs on Mac/Linux - Utilities for conversion to/from mmCIF General: ======== - Multiple bug fixes - 64-bit Windows 7 installer - Improved bulk solvent mask calculations (phenix.refine, phenix.maps, etc.): - analyzes mFo-DFc map to identify spurious negative density blobs in bulk solvent regions and applies correction, can decrease R-factors by 0.5-2.0% Refinement: =========== - phenix.refine: - bug fixes in occupancy refinement, hydrogen addition - new local and global real-space refinement (RSR) methods: - Global RSR (refine all atoms, as before) runs only if: d_min > 1.5, r_work > 0.25, and not neutron data or "individual_sites_real_space" is the only selected strategy - Local RSR: residue-by-residue, replaces old fix_rotamers option - fits both main chain and sidechain - only applies to residues with rotamer outlier, poor CC, or clashes - new residue fit serves as torsion restrains for subsequent macro-cycle - normally not performed when explicit hydrogens present - added omit_selection keyword: sets atom occupancies for a selection to zero prior to refinement - optional harmonic restraints on starting positions - used to maintain structure close to starting model during simulated annealing omit map calculation - alpha feature: placement of elemental ions (place_ions=True) - looks for Mg, Cl, Ca, and Zn by default; specify elements=Cl,Ni,... to give explicit list (recommended) - works best with anomalous data Experimental Phasing and Model Building: ======================================== - AutoSol: - overall_best_refine_data.mtz now contains uncorrected F+,sigF+,F-,sigF- data and uncorrected FP,SIGFP. Previously only the FP,SIGFP was uncorrected, and F+,sigF+,F -,sigF- had been corrected for anisotropy and sharpened. Note that output map files from phenix.autosol and phenix.autobuild are still sharpened and corrected for anisotropy. - For MIR, if quick=True then as soon as a good solution is found with HySS all other derivatives are solved by difference Fouriers. This can speed up MIR structure solution. You can disable this feature with skip_hyss_other_derivs_if_quick=False. - AutoSol and AutoBuild: - It is now possible to specify a different number of copies of different chains in the sequence file. If the sequence file has n copies of chain A and m of chain B, it is now assumed that the stoichiometry is ncs_copies * (nA, mB). Previously it had been assumed always that the stoichiometry was ncs_copies *(A, B). - For structure determination with extremely little phase information there is a new keyword extreme_dm=True (default is False). This allows density modification to use parameters optimized for very poor phasing if the FOM of phasing is less than fom_for_extreme_dm. - AutoBuild - phenix.autobuild now requires that if a hires (or refinement) file is supplied, it must have a complete set of free R flags (test set) if the datafile also has a test set. In this case the test set from the datafile is ignored and the one from the hires/refinement file is used. - You can use the Phenix GUI to extend the test set from your datafile to match the data in your hires/refinement file if necessary. Molecular Replacement: ====================== - Phaser: - various speed enhancements - new normal modes analysis features for domain finding (phaser.splitter) - bug fixes - MR-Rosetta: - You can now tell mr_rosetta to ignore long-running sub-processes and just go on with the finished jobs. New commands: ============= - phenix.dynamics (new command): - simple Cartesian dynamics, replaces equivalent function in PDBTools - phenix.parallel_autobuild (new command): - a tool for running phenix.autobuild many times in parallel, picking the best results, and iterating with the new maps as a starting point. - can make effective use of as many as 40 processors. Ligands: ======== - phenix.ligand_pipeline: - numerous bug fixes - more flexible handling of input sequence files - optional Sculptor step prior to MR to fix residue identities - sidechain pruning enabled by default - interactive mode now includes ligand selection - phenix.guided_ligand_replacement: - Guided Ligand Replacement (GLR) can now search for a protein-ligand complex suitable for the guided fitting using web services on the PDB website or in a local directory. - GLR ligand input has been reworked to allow the use of the three-letter code relying on eLBOW to generate the restraints. - REEL: - simplification and improvement of molecule building - support for cis/trans E/Z enantiomers - view .geo files Miscellaneous: ============== - PDBTools: - simple dynamics option moved to new command, phenix.dynamics - remove_alt_confs and truncate_to_poly_ala options made compatible with other model modifications - HySS: - converted to use standard Phenix parameter syntax - Many new optional features: - Parallel pre-scoring of 2-site solutions - Parallel completion and scoring - Comparison with a fixed solution - Resolution cutoff for Phaser rescoring - Top-scoring solution written even if no matches found - All solutions written - Skip direct methods completion - LLG completion sigma cutoff - Scoring of input sites - Randomization of input sites 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 Building 80, Room 247 Building 978, Room 4126 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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bad density for part of the electron density map
by Wei Shi 08 Oct '13

08 Oct '13

Hi all, I am working with a dataset in space P212121, resolution 2.8 amstrong, total completeness of the data 96.2% (98.1%), I/sigma 5.2 (3.1). This is a structure of a transcriptional factor (dimer) with the ligand. Upon ligand binding, there is conformational change in some part of the protein and I used the apo protein structure as a search model, and get a molecular replacement solution. After some rounds of refinement and rebuild (mainly in a region in the C-terminal ligand binding domain), the best refinement I have is as follows. But the electron density map for the C-terminal DNA binding (about 80 residues) is still very bad.... I tried to mutate them to alanine and do refinement and also tried to delete the whole region to do refinement, but both of the strategies didn't give me better density which I could use to rebuild the residues manually. I am wondering whether any of you have any ideas about what might go wrong and any suggestions about what to check or try next. Thank you so much! start final --------------------------------------- R-work: 0.3220 0.3100 R-free: 0.3916 0.3884 RMS(angles): 2.50 1.39 RMS(bonds): 0.016 0.010 Ramachandran outliers: 1.8% (Goal: < 0.2%) Ramachandran favored: 89.0% (Goal: > 98%) Rotamer outliers: 5.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 11.50 Overall score: 2.71 Best, Wei

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