- phenixbb - phenix-online.org

Different R-free values
by Jerome Nwachukwu 10 May '11

10 May '11

Dear all: I find that phenix.refine reports a higher starting R-free than those stated for structures downloaded from the PDB. For instance, the R-free stated in the PDB = 0.287, using Polygon = 0.2880, but the Start R-free from phenix.refine = 0.3114 Is this usual, or is something seriously wrong? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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error from loop fitting
by Kendall Nettles 09 May '11

09 May '11

I'm trying the loop fitting for the first time and keep getting this error: Reading in sequence probability info and matching to input PDB List of segments read from input PDB file: Segment 0 Start: 225 End: 380 ChainID: 'A' NO MATCH What should be in the sequence file? it is fasta format?it is the entire sequence, or just the loop? I've played with different combinations and keep getting the same error. Best regards, Kendall Nettles

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Diffraction anisotropy
by Ina Lindemann 06 May '11

06 May '11

Hi, I am refining a structure of 2.3A resolution. The R values with and without bulk solvent and anisotropic scale are quite different as you can see here: Start R-work = 0.3751, R-free = 0.5562 (no bulk solvent and anisotropic scale) Final R-work = 0.3741, R-free = 0.5557 (no bulk solvent and anisotropic scale) Start R-work = 0.2298, R-free = 0.2974 Final R-work = 0.2261, R-free = 0.2970 I checked the anisotropy of the data with different tools: Results from Xtriage: Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of None: 39.25 A**2 Estimated -log of scale factor of None: -2.59 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of None: 50.10, 0.00, 0.00 50.10, -0.00 25.47 Equivalent representation as U_cif: 0.63, -0.00, -0.00 0.63, 0.00 0.32 Eigen analyses of B-cart: Value Vector Eigenvector 1 : 50.103 ( 0.71, 0.71, -0.00) Eigenvector 2 : 50.103 (-0.71, 0.71, -0.00) Eigenvector 3 : 25.473 (-0.00, 0.00, 1.00) ML estimate of -log of scale factor of None: -2.57 Correcting for anisotropy in the data Results from PHASER: Principal components of anisotropic part of B affecting observed amplitudes: eigenB (A^2) direction cosines (orthogonal coordinates) 8.178 0.9961 0.0879 0.0000 8.178 -0.0879 0.9961 0.0000 -16.357 -0.0000 -0.0000 1.0000 Anisotropic deltaB (i.e. range of principal components): 24.535 Results from Ctruncate: ANISOTROPY CORRECTION (using intensities): Anisotropic scaling (orthogonal coords): | -0.2272 -0.0000 -0.0000 | | -0.0000 -0.2272 0.0000 | | -0.0000 0.0000 0.4543 | Anisotropic U scaling (fractional coords): | -4.451e-05 -5.622e-23 -1.266e-21 | | -5.622e-23 -4.451e-05 -8.929e-22 | | -1.266e-21 -8.929e-22 4.717e-06 | Anisotropic B scaling (fractional coords): | -3.514e-03 -4.439e-21 -9.995e-20 | | -4.439e-21 -3.514e-03 -7.050e-20 | | -9.995e-20 -7.050e-20 3.725e-04 | Eigenvalues: 0.7728 0.7728 1.4543 Eigenvalue ratios: 0.5314 0.5314 1.0000 Resolution limit in weakest direction = 3.156 A Now I am not sure about the severeness of anisotropy and the necessary procedure and would be very pleased if anyone could help. The electron density maps look okay related to the resolution. Has anyone experience with the diffraction anisotropy server or ellipsoidal truncation with data with comparable anisotropy? Thank you for your help in advance Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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phenix.mr_rosetta error
by Jermaine Jenkins 05 May '11

05 May '11

Hi, I am trying to use phenix.mr_rosetta supplying a local.hhr file and using only the top alignment which is an NMR structure and the pre_refine option. It finishes the mr.model_preparation and writes out two pdbs ( _sculpt and _chain that each have 10 ensembles) but then writes out a empty alignment.ali file (should be 100% identity between the template and the search model). Below is the error I get in the RUN_1.log file. Wrote dummy alignment to /pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali ******************* ERROR ENDING *************** Sorry, the alignment file ['/pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' ******************* ERROR ENDING *************** Sorry, the alignment file ['../pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' Thanks, JJ

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Off topic: Apologize for linkedin invitation accident
by Nian Huang 03 May '11

03 May '11

Dear fellows, I am really sorry for the massive invitations from my linkedin account. I was certain that I skipped the sending invitation step from my contact lists and I am not sure how it could still happen in the end. Please delete those emails as you wish and I thank the people who have already added me to the connection. Nian Huang, Ph.D. Dept. of Biochemistry UT Southwestern Medical Center

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Invitation to connect on LinkedIn
by Nian Huang via LinkedIn 03 May '11

03 May '11

LinkedIn ------------Nian Huang requested to add you as a connection on LinkedIn: ------------------------------------------ Felix, I'd like to add you to my professional network on LinkedIn. - Nian Accept invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… View invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… ------------------------------------------ Why might connecting with Nian Huang be a good idea? Have a question? Nian Huang's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Nian Huang and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation

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Sulfate ion on 2-fold axis
by J. Fleming 01 May '11

01 May '11

Hi all, I have a sulfate ion sitting on a 2-fold axis of symmetry. If I set all the atom occupancies to 0.5 and refine using phenix.refine (Phenix v. 1.5-2) the occupancies are changed to 0.00 for the sulfur, 1.00 for three of the oxygen's, and 0.72 for the fourth oxygen. Can anyone explain this? Thanks in advance, Jon

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Phenix version 1.7.1 released
by Paul Adams 29 Apr '11

29 Apr '11

The Phenix developers are pleased to announce that version 1.7.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical Interface ------------------- - New interfaces for: phenix.phase_and_build, phenix.mtz2map, phenix.french_wilson - Updates to the Structure comparison GUI, which now allows use of non-identical sequences, and results viewing in PyMol. - A plugin for running multiple sequence alignment Installers ---------- - Graphical installers for Macintosh (installs in /Applications) - Binary installer for 64-bit Mac Intel (OS 10.6 only) New Commands ------------ - phenix.french_wilson (new command): - Implements French & Wilson correction of negative and weak intensities (see Acta Cryst A34:517 [1978]) - outputs modified amplitudes in MTZ format - used internally by default in Phaser GUI and phenix.refine when intensities are provided - phenix.reciprocal_space_arrays (new command): - this tool takes a PDB model and a data file and outputs an MTZ file containing a number of arrays that are typically used in various crystallographic calculations, such as R-factors, maps, refinement targets, etc. The output arrays include: - Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, Hendrickson-Lattman coefficients (input original, computed from model and combined), FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more - phaser.brunett (new command): - automated molecular replacement using incremental exploration, with support for parallelization - quick SSM-superposition-based LLG evaluation for alternative models for the same component - "puzzle"-assembly of solutions for a more complete solution - novel space group determination algorithm that retains possible space groups until they are significantly outperformed by others - handles custom models (used without modification), templates (a PDB template and an alignment, Sculptor is run to create models from it) and homology searches (PDB and alignment obtained from homology search, currently HHPRED and BlastXML; data downloaded from EBI) Structure refinement -------------------- - New output MTZ file that contains original data, amplitudes used in refinement, and map coefficients (this replaces *_map_coeffs.mtz) - French and Wilson procedure automatically applied if intensities are input to refinement - Optional automatic rigid-body grouping by polymer chain (rigid_groups_mode=one_group_per_chain) - Reference model uses a "top-out" restraint potential with a smooth cutoff - Automatic determination of Saenger class for nucleic acid base pairs (if not provided by user) - Ability to run phenix.find_tls_groups internally to obtain atom selections - option: tls.find_automatically=True - Automatic non-bonded distance correction for H-bonded atoms Molecular Replacement --------------------- - phenix.mr_rosetta: - Bug fixes - Added web site with data used in Nature Rosetta+Phenix paper at: http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/ - Added keyword include_solvation_energy=False to allow use of mr_rosetta for membrane proteins. - phenix.automr: - bug fix in residue number input, now allows four-digit IDs Ligands ------- - eLBOW: - Geometries can be generated using CSD Mogul substructure searches of experimental geometries. Estimated standard deviations of the bonds and angles are also included in the restraints file. Visualization ------------- - KiNG (phenix.king): - Improved opening multiple electron density maps: tiered windows, with automatic deciphering of file name to preset sigma levels and colors. - Added -phenix command line option to preset map colors to be more like Coot. 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 Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology 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: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

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TLS group definition
by Andres Palencia 28 Apr '11

28 Apr '11

Dear All, I am trying to refine using TLS parameter as in the attached file generated in ccp4. my protein contains a core part from where are inserted several domains. I am defining each of the insertions as a group and this is fine. The problem comes when I try to define the core protein (discontinuous residue ranges). As example, I want to define residues 1:230, 416:568, 629:794 in chain A of the protein; and in the same group I would like also to include 3 bases of RNA, bases 84-87 of chain B. I have seen several questions related to TLS definitions in the archive mailing list, including an answer from Anastasis Perrakis with files attached which I can not extract, but so far I have not find the solution. Could anybody help on that? thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

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phenix.maps
by Bradley Hintze 27 Apr '11

27 Apr '11

This shows my ignorance about mtz files. I'm having trouble with phenix.find_helices_strands. I got 3kat.mtz from Pavel's database. I run: $ phenix.find_helices_strands 3kat.mtz labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" and get: PHENIX find_helices_strands Wed Apr 27 13:12:19 2011 Commands: phenix.find_helices_strands 3kat.mtz labin=LABIN FP=2FOFCWT PHIB=PH2FOFCWT # find_helices_strands # # Find secondary structure in a map defined by map coeffs in an input mtz file. # Type phenix.doc for help Input map resolution is 3.1 A Labin line will be: LABIN FP=2FOFCWT PHIB=PH2FOFCWT To change it modify this by specifying FP= and PHIB= [and optionally FOM=] like this: labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" Map from: TEMP_3kat.mtz using labin LABIN FP=2FOFCWT PHIB=PH2FOFCWT NOTE: ratio_trace_extra increased to 1.3 A as dmin > 3.0 NOTE: rad_sep_trace increased to 0.6 A as dmin > 3.0 Fixing sampling interval rad_sep_trace= 0.6 A Optimizing CA-CA tolerance to obtain ratio of 4.0 for nonamers:atoms Tracing chains at resolution of 3.1 A CCP4: Error in label assignments in LABIN

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