- phenixbb - phenix-online.org

mr_rosetta
by Jermaine Jenkins 11 May '11

11 May '11

I have been trying a standard run of mr_rosetta and I have stopped at the same point (output below). 32 folders were created in the GROUP_OF_RESCORE_MR_ROSETTA_1 folder and the mr_rosetta.log files all say that saved overall results to a .../results.pkl and the Run log file states that each job finished. But no further files were written in the Work folder under each RUN folder and I am assuming there should be a folder with my final 20 Rosetta models somewhere. Does this mean there was a failure in a subscript? ============================================================================== Starting sub-processes Group of rescore MR rosetta:Rescoring set of rosetta models... ============================================================================== Splitting work into 32 jobs and running with 4 processors using sh background=True in ....MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1 Starting job 1...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log Starting job 2...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log thanks, JJ

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Low Resolution Density Modification Problems
by Ian Slaymaker 10 May '11

10 May '11

I am having a problem getting a decent DM map at lower resolutions (8, 10, 12, 20). We have a model for the data (R-factor ~34) at 6.6 A (the model is based on different higher resolution data), and when I try and do DM at anything worse than 6.6, the density no longer covers the model. Any suggestions would be appreciated. Ian Slaymaker USC <http://www-scf.usc.edu/%7Eslaymake/>

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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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Question regarding phenix.fmodel
by zhangh1＠umbc.edu 26 Apr '11

26 Apr '11

Hi, According to the instruction, phenix.fmodel was supposed to calculate Fc only; however, when I try the following 2 scripts, they ended up with different Fc values (at the same hkl point): 1. phenix.fmodel ${PDB} high_resolution=XX 2. phenix.fmodel ${PDB} ${MTZ} The instruction says (2) will output Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file, so I thought 1 and 2 should have the same values at the same hkl points... One more question about fmodel. I have 2 models with different sizes, and want to compare their Fc in the same scale. If I use (1), there will be no scaling by default I think, so the Fc results can be directly compared, right? (A most direct way would be checking the Fc at h0k0l0 point and see whether they are proportional to the molecular size, but it seems phenix.fmodel will ignore this point even I expicitly add it to the MTZ file.) Thanks! Hailiang

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Residue number error after autoMR or PhaserMR
by Zhang yu 23 Apr '11

23 Apr '11

Hi, When I run MR in Phenix, I found that there is a numbering error in the solution PDB file The error is that Phenix numbers residues from 0 again when the residue numbers are over 999, though they belong to the same chain. For example "ATOM 11504 N HIS C 999 -37.389 50.436 57.144 1.00 56.62 N ATOM 11505 CA HIS C 999 -36.908 51.569 57.924 1.00 60.55 C ATOM 11506 C HIS C 999 -37.438 51.479 59.337 1.00 61.73 C ATOM 11507 O HIS C 999 -38.648 51.484 59.549 1.00 60.99 O ATOM 11508 CB HIS C 999 -37.382 52.895 57.326 1.00 63.09 C ATOM 11509 CG HIS C 999 -36.353 53.577 56.478 1.00 66.67 C ATOM 11510 ND1 HIS C 999 -35.280 52.912 55.925 1.00 68.12 N ATOM 11511 CD2 HIS C 999 -36.247 54.865 56.070 1.00 68.95 C ATOM 11512 CE1 HIS C 999 -34.559 53.762 55.214 1.00 69.21 C ATOM 11513 NE2 HIS C 999 -35.122 54.953 55.285 1.00 69.80 N ATOM 11514 N MET C 0 -36.544 51.378 60.309 1.00 64.17 N ATOM 11515 CA MET C 0 -36.992 51.355 61.688 1.00 66.45 C ATOM 11516 C MET C 0 -37.290 52.797 62.083 1.00 68.10 C ATOM 11517 O MET C 0 -37.018 53.716 61.302 1.00 68.58 O ATOM 11518 CB MET C 0 -35.903 50.763 62.605 1.00 67.35 C ATOM 11519 CG MET C 0 -36.051 49.272 62.997 1.00 67.14 C ATOM 11520 SD MET C 0 -36.534 48.947 64.735 1.00 65.84 S ATOM 11521 CE MET C 0 -35.169 49.744 65.675 1.00 66.20 C ATOM 11522 N VAL C 1 -37.840 53.015 63.272 1.00 69.46 N ATOM 11523 CA VAL C 1 -38.160 54.373 63.711 1.00 69.99 C ATOM 11524 C VAL C 1 -36.911 55.251 63.875 1.00 70.28 C ATOM 11525 O VAL C 1 -37.029 56.452 64.122 1.00 70.20 O ATOM 11526 CB VAL C 1 -38.908 54.379 65.057 1.00 70.57 C ATOM 11527 CG1 VAL C 1 -40.322 53.847 64.873 1.00 71.16 C ATOM 11528 CG2 VAL C 1 -38.148 53.537 66.061 1.00 70.54 C" Does anyone has idea about it? Thanks Yu Zhang

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fwd: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011
by Nathaniel Echols 22 Apr '11

22 Apr '11

---------- Forwarded message ---------- From: Bi-Cheng Wang <wang(a)bcl1.bmb.uga.edu> To: phenixbb(a)phenix-online.org Date: Fri, 22 Apr 2011 12:13:02 -0400 Subject: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011 We would like to call your attention to a workshop associated with the upcoming 2011 APS Users Meeting, which will be held on May 4, 2011 at the APS, Argonne National Laboratory, USA. The title of the workshop is “Soft X-ray Crystallography”. You may find the workshop program at http://2011usersmeeting.conference.anl.gov/APSWK1Agenda.htm The web links for meeting registration and the application for a permit to enter the Argonne National Laboratory are: https://2011usersmeeting.conference.anl.gov/register http://www.aps.anl.gov/Users/Site_Access We hope you will be able to attend the APS Users Meeting and our workshop. All the best, B.C. Wang, John Rose, Gerd Rosenbaum and John Chrzas

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b factors reporting
by Maia Cherney 22 Apr '11

22 Apr '11

To: PHENIX user mailing list<phenixbb(a)phenix-online.org> Date: Thu, 21 Apr 2011 15:09:19 -0600 Subject: Re: [phenixbb] B factor for DNA and Protein Pavel Afonine wrote: > > Yes, this trivial combination of two commands will do it: > > phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb > phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb > phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb > Dear Pavel, These commands did not work for me (version 1.7-650). I need to report average b factors separately for the protein, water, several ligands and ions, all of them in one chain A. Traceback (most recent call last): File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/pdbtools.py", line 3, in<module> from mmtbx import pdbtools File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/__init__.py", line 3, in<module> import cctbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx/cctbx/array_family/flex.py", line 1, in<module> import scitbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx/scitbx/array_family/flex.py", line 2, in<module> import boost.optional File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/optional.py", line 1, in<module> import boost.python File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in<module> ext = import_ext("boost_python_meta_ext") File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib/libboost_python.so: undefined symbol: PyUnicodeUCS2_AsWideChar sys.path: /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/iotbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/PyCifRW /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/source/phaser /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/libtbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/share/python /usr/lib/python2.6 /usr/lib/python2.6/plat-linux2 /usr/lib/python2.6/lib-tk /usr/lib/python2.6/lib-old /usr/lib/python2.6/lib-dynload /usr/lib/python2.6/dist-packages /usr/lib/python2.6/dist-packages/Numeric /usr/lib/python2.6/dist-packages/PIL /usr/lib/python2.6/dist-packages/gst-0.10 /var/lib/python-support/python2.6 /usr/lib/python2.6/dist-packages/gtk-2.0 /var/lib/python-support/python2.6/gtk-2.0 /usr/local/lib/python2.6/dist-packages

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Creating cif file of ligands by Elbow/ReadySet
by Ngan Nguyen Bich 21 Apr '11

21 Apr '11

Dear Phenix developers, I'm quite new in crystallography and use PhenixGUI for refinement my protein. I got a problem when I had to create cif file of the new ligand to feed in phenix_refine by Elbow/ReadySet I saw that program creates some bonds shorter or longer compared to the statistic value from the CSD for example. Here are some examples when I play with Elbow (same problem with ReadySet) 1. when I feed program the chemical string, (template PDB file is the mylidand_idea.pdb) CR2 C3 CA3 single 1.569 0.038 and if I choose AM1 optimization CR2 C3 CA3 single 1.602 0.040 2. when I feed program the .pdb file, choose Use geometry for Initial geometry. GYC N CA1 single 1.409 0.020 * GYC N HN1 single 0.902 0.020 GYC N HN2 single 0.901 0.020 GYC SG1 CB1 single 1.797 0.020 GYC SG1 HG1 single 1.204 0.020 GYC CB1 CA1 single 1.500 0.020 GYC CB1 HB11 single 1.006 0.020 GYC CB1 HB12 single 0.972 0.020 GYC CA1 C1 single 1.528 0.020 GYC CA1 HA1 single 1.010 0.020 GYC C1 N2 aromatic 1.412 0.020 GYC C1 N3 aromatic 1.304 0.020 GYC N2 CA2 aromatic 1.505 0.020 ** GYC N3 C2 aromatic 1.349 0.020 GYC N3 CA3 single 1.423 0.020 GYC C2 O2 double 1.370 0.020 GYC C2 CA2 aromatic 1.509 0.020 GYC CA2 CB2 single 1.532 0.020 GYC CA3 C single 1.496 0.020 It's strange to me when comparing * and ** and if I run AM1 GYC CB1 CA1 single 1.533 0.035 GYC CA3 C single 1.564 0.035 as I know, the C-C single bond should be about 1.51. Does anyone get a problem like me? I wonder if I didn't do properly or some thing else, or any suggestion for my case. One more questions is that afterward I found cif file (seemly mmcif file) of my ligand in phenix-1.7-650/chem_data/chemical_components And I'm wondering that How the program use these cif file, or I can use them in which way? Thank you in advance. Best regards, Ngan Nguyen Bich KULeuven Belgium

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unit cell discrepancies
by Michael Hothorn 21 Apr '11

21 Apr '11

Dear all, I am sure there is a simple explanation for this, but I cannot find a solution. I am reading in an .mtz file in phenix.refine. mtzdump reports the following unit cell constants on the file test.mtz itself: 175.0930 67.2510 119.0500 90.0000 121.5500 90.0000 The refined .pdb file and .maps report however a slightly different unit cell, as does the logfile >snip Miller array info: test.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=39702 Type of sigmas: double, size=39702 Number of Miller indices: 39702 Anomalous flag: False Unit cell: (175.17, 67.236, 119.246, 90, 121.416, 90) What am I missing? Thanks! Michael

6 16

Installation issue
by Simon Kolstoe 21 Apr '11

21 Apr '11

Hi, I've just installed the latest stable version of phenix on a new macbook pro using phenix-installer-1.7-650-mac-intel-osx.tar However, as I like running phenix.refine on the command line, I normally source the script phenix_env.sh which on my other computer is in the directory /Applications/PHENIX-1.7-650/Contents/phenix-1.7-650/ However the latest install doesn't seem to have the final phenix-1.7-650 directory! Has phenix_env.sh moved somewhere else and if so where? Thanks, Simon

2 2

Out of Memory Errors
by Heather Condurso 21 Apr '11

21 Apr '11

Hello all, I am currently running the Phenix GUI version 1.7-650 on an iMac with an 3.2Ghz Intel Core i3 processor, 8GB of memory operating under OS 10.6. During many of my runs (mostly AutoMR runs but sometimes refine) I get out of memory errors. I have my system booted in 64 bit mode and I watch the activity monitor and find that phenix doesn't use much more than 2GB of memory. My search model is very large. My unit cell contains 4 trimers (each monomer is 48kDa). I hadn't encountered this issue until I began to increase my search model from one trimer to four. Do you have any suggestions as to how I could avoid this error without minimizing my search model? Often my AutoMR runs get the out of memory error at the start of refinement, but just now the memory was exhausted during the fast rotation function. During this run I used all default parameters with a max res of 4.0 and RMSD of 1.0. Any advice you can give would be greatly appreciated! Heather

3 2

R free test set size
by Yuri 21 Apr '11

21 Apr '11

hello everyone, I just noticed that the latest model I am working on has only 2% of reflections marked as free R after refinement! I usually give the GUI the .sca files out of HKL2000 that do not have an Rfree array pre-defined. The GUI lets you know about the lack of it and asks me if I want generate a test set of 10%. I say yes. However the pdb header shows the only 2.14% are chosen for free R. I see that some of my other models (lower resolution) have test arrays of around 7-10% as I would expect. How can I explicitly define the size I want? Thanks -- Yuri Pompeu

2 1

optimizing weights
by Alexandra Deaconescu 20 Apr '11

20 Apr '11

Dear all: I would like to optimize my weights during Phenix refinement. I am running Phenix 1.6.4-486 using the gui, and I have checked the "optimize weights", but I cannot see the results of the optimization in the output, so I do not know the relationship between Rfree/geometry and wc and wxc_scale (I might not want to pick the automatically selected wxc_scale for the lowest Rfree, but would like to find a reasonable values to give me good geometry). Some earlier posts indicated that this is not output in the log file, but I am running a more recent version... Also, in case I wanted to adjust the weights manually, do I have set wxc_scale AND check the fix wc at the same time in the gui? Or just one of them? What would be typical values to start with at 2.8A (even if the answer depends on the particular data)? Same question for the ADP refinement.... I am working at 2.8A and my B factors are high (higher I think than what one would expect at this resolution). Thanks for your help, Alex -- Alexandra M. Deaconescu, Ph.D. Research Associate, HHMI c/o Grigorieff Laboratory Rosenstiel Center MS029 Brandeis University 415 South St. Waltham, MA 02454 phone: 781-736-2498 For FEDEX Brandeis University Kalman Receiving Dock 415 South St. Waltham, MA 02454

2 1

obtaining f'/f'' from solved structures and comparison to a fluorescence scan
by Francis E Reyes 20 Apr '11

20 Apr '11

Hi phenixer's I'm in need of reliable f'/f'' for my heavy atom (that isn't Sasaki tables which I believe is for free, unbound atoms). I've used group_anomalous in phenix.refine before so I'm sure a phenix utility is capable of extracting it. I wanted to if it's possible to extract it from several solved structures (I have the DANO/SIGDANO, F(+)/F(-), or if needed the original I(+)/I(-)) I'm curious to see if there's wide variation and whether it'd be as reliable (or even better) than actually taking a fluorescence scan (and of course use the values for my current phasing challenge as a starting point). F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

AutoSol
by Nora Cronin 18 Apr '11

18 Apr '11

Is have 2 difference anomalous datasets with two different heavy atoms. I can input 2 SAD datasets in AutoSol using the Wavelength and Group = keywords. How do I input 2 different crystal_info keywords since this keyword does not accept the Group= option? cheers Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

1 0

unusual maps and Rfree for 1.75 structure
by Yuri 18 Apr '11

18 Apr '11

>>you did not mention the resolution... From your email I guess it is 1.9A, is it correct? It is 1.75A. But like I said the maps right now do not look like those of 1.75 resolution. my 1.9 maps looked way better... The P1 strategy is valid. I will also try processing without the screw axis P 4 2 2, or maybe even P 4 21 2. It looks like the other systematic absences are ok (they are pretty weak reflections). -- Yuri Pompeu

1 0

unusual maps and Rfree for 1.75 structure
by Yuri 17 Apr '11

17 Apr '11

I am solving a structure of an enzyme that I have solved many times before, the only difference is a single mutation in the active site. The crystal grew in basically exact conditions (macroscopically speaking they look different) as the other mutants I had. I scaled the data P 43 21 2 Rsym 0.068. Like all the other data sets I had before. This time however, the initial model has Rfree of about 0.27 and the maps look more like those of a 2.5 - 2.8 structure. My experinence with this enzyme is that I should be looking at around 0.22 or lower Rfree, and pretty clear maps as I saw for my 1.9 structure. Xtriage does not detect any pathologies. I rececked my scaling log file, and it lists the systematic absences for the data. I see some that are not that "weak" for instance : h k l I/sigma 0 0 1 6.0 0 0 2 5.8 0 0 13 7.8 So I am inclined to reprocess my data in P 4 2 2. Are these "symptoms" of a possible wrong space group assignment? Is there something else obvious I am overlooking? Thank you -- Yuri Pompeu

3 2

Re: [phenixbb] Autobuild error -- merging results of nearly-finished OMIT and autobuild runs
by Thomas C. Terwilliger 15 Apr '11

15 Apr '11

Dear Nick, I'm sorry for the error ("[Errno 5] Input/output error") that you are getting with your i7-based PC's with Fedora 14. I have not seen this error before, but we can try to debug it with "debug=true" and also I have a work-around for combining the files that you already have created so you don't need to rerun your whole jobs. Can you possibly run this quick test job to try and get it to fail: phenix.autobuild $PHENIX/phenix_regression/wizards/perfect.mtz \ input_labels="FP SIGFP" \ map_file=$PHENIX/phenix_regression/wizards/perfect.mtz \ input_map_labels="FP PHIC FOM" \ seq_file=$PHENIX/phenix_regression/wizards/seq.dat \ resolution=3.0 \ solvent_fraction=.6 \ model=$PHENIX/phenix_regression/wizards/coords.pdb \ rebuild_in_place=True \ n_cycle_rebuild_min=1 \ n_cycle_rebuild_max=1 \ multiple_models=True \ multiple_models_number=1 \ multiple_models_group_number=2 \ highest_resno=200 \ debug=true This takes about 5 minutes. If it fails, can you send me (terwilliger(a)lanl.gov, not the list) the end out the output where it gives a traceback of where the error occurred? Combining files from a nearly-complete autobuild run with rebuild-in-place=true You can combine models with autobuild, providing all models have exactly the same set of atoms (aside from any solvent) by editing this script (basically you run a dummy autobuild run to create a directory and database entries, then you copy your files there, then you run autobuild and tell it to carry on and do the combine step): -------------------------------------------------------- #!/bin/csh -f #COMBINE_MODELS SCRIPT if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1>& dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT ------------------------------------------------------- Combining OMIT runs that have been run on separate computers or that come from a nearly-completed omit run: You can do this by copying all the individual mtz files with map coefficients for omit regions to a single directory and running a script like this one: (NOTE: you need to ensure that the OMIT regions are defined the same in the runs where you got your overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc files and this run. You ensure that with the n_xyz command that sets the grid. You can copy this from one of your resolve log files created when you ran your omit (i.e., AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0/resolve.log will have a line "nu nv nw: 32 32 32 " and you copy those numbers). ------------------------------------ #!/bin/csh -f # COMBINE OMIT SCRIPT phenix.resolve<<EOD hklin exptl_fobs_phases_freeR_flags.mtz labin FP=FP SIGFP=SIGFP n_xyz 32 32 32 # YOU MUST SET THIS BASED ON THE nu nv nw in a resolve log file. solvent_content 0.85 no_build ha_file NONE combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_13 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_14 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_15 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_16 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_17 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_18 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_19 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_20 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_21 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_22 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_23 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_24 omit EOD # END OF COMBINE OMIT SCRIPT All the best, Tom T >> Dear Phenix Developers, >> >> I have been experiencing problems with autobuild whenever I try to rebuild >> an MR model or calculate a composite OMIT map. These tasks always end the >> same way: with "[Errno 5] Input/output error". The failure always happens >> when the run is basically finished and trying to combine the output from >> multiple tasks. My first thought was that my hard drive was full or fixing >> to crash, but these problems happen across several machines and have persisted through multiple official and nightly Phenix releases (currently >> running 1.7-634). The computers that cannot run autobuild successfully are >> both core i7-based PCs running Fedora 14 (though these problems also occurred running earlier Fedora versions). My older xeon-based PC runs autobuild without any trouble, which makes me think this a core i7-related >> problem. I have searched the PhenixBB archive and have not turned up any >> similar problems - have any other users experienced trouble with Phenix and core i7? Is there a work-around I ca >> n use to manually combine the various outputs? The core i7 machines are >> so much faster, I would really like to solve this problem so that I can stop relying on my aging xeon PC for these long calculations. I have included the end of two log files for reference. Also, autosol runs fine >> on the core i7 computers and successfully builds wonderful models from my >> SeMet SAD data. Thank you for Phenix and for any advice you can give. >> >> Best wishes, >> Nick Silvaggi >> >> P.S. I apologize if this message appears twice - I sent it once from an address that was not registered with the BB and decided to re-send from a >> registered address. >> >> Autobuild after MR: >> ----------------------------------------------------------------------------------------------------- Standard build in parallel starting with refine.pdb_1 >> This is the first try at building this model >> Try: 1 building 1 model >> Try: 2 building 1 model >> Try: 3 building 1 model >> Running up to 3 jobs in parallel... with total of 3 jobs >> >> Splitting work into 3 jobs and running with 3 processors using sh background=True in >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0 >> >> Starting job 1...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log Collecting all runs now >> *************ERROR ENDING ******************* >> >> ******************************************************************************** Failed to carry out AutoBuild_build_cycle: >> >> [Errno 5] Input/output error >> ******************************************************************************** >> >> *************ERROR ENDING ******************* >> >> >> Calculating SA composite omit map: >> ----------------------------------------------------------------------------------------------------- Starting job 34...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log Starting job 35...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log Starting job 36...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log Collecting all runs now >> *************ERROR ENDING ******************* >> >> ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: >> >> [Errno 5] Input/output error >> ******************************************************************************** >> >> *************ERROR ENDING ******************* >> >> Nicholas R Silvaggi, Ph.D. >> University of Wisconsin, Milwaukee >> Department of Chemistry and Biochemistry >> 3210 North Cramer St >> Milwaukee, WI 53211 >> >> Office: Chemistry 272B >> Phone: 414-229-2647 >> silvaggi(a)uwm.edu >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

Autobuild error
by Nicholas R Silvaggi 15 Apr '11

15 Apr '11

Dear Phenix Developers, I have been experiencing problems with autobuild whenever I try to rebuild an MR model or calculate a composite OMIT map. These tasks always end the same way: with "[Errno 5] Input/output error". The failure always happens when the run is basically finished and trying to combine the output from multiple tasks. My first thought was that my hard drive was full or fixing to crash, but these problems happen across several machines and have persisted through multiple official and nightly Phenix releases (currently running 1.7-634). The computers that cannot run autobuild successfully are both core i7-based PCs running Fedora 14 (though these problems also occurred running earlier Fedora versions). My older xeon-based PC runs autobuild without any trouble, which makes me think this a core i7-related problem. I have searched the PhenixBB archive and have not turned up any similar problems - have any other users experienced trouble with Phenix and core i7? Is there a work-around I can use to manually combine the various outputs? The core i7 machines are so much faster, I would really like to solve this problem so that I can stop relying on my aging xeon PC for these long calculations. I have included the end of two log files for reference. Also, autosol runs fine on the core i7 computers and successfully builds wonderful models from my SeMet SAD data. Thank you for Phenix and for any advice you can give. Best wishes, Nick Silvaggi P.S. I apologize if this message appears twice - I sent it once from an address that was not registered with the BB and decided to re-send from a registered address. Autobuild after MR: ----------------------------------------------------------------------------------------------------- Standard build in parallel starting with refine.pdb_1 This is the first try at building this model Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 3 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running with 3 processors using sh background=True in /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0 Starting job 1...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log Collecting all runs now *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: [Errno 5] Input/output error ******************************************************************************** *************ERROR ENDING ******************* Calculating SA composite omit map: ----------------------------------------------------------------------------------------------------- Starting job 34...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log Starting job 35...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log Starting job 36...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log Collecting all runs now *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: [Errno 5] Input/output error ******************************************************************************** *************ERROR ENDING ******************* Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211 Office: Chemistry 272B Phone: 414-229-2647 silvaggi(a)uwm.edu

1 0

parallel structure comparison
by Kendall Nettles 14 Apr '11

14 Apr '11

Dear PHENIX developers, In this weeks build, when I launch coot from the structure comparison results, no models or maps are loaded. It works in the last major release. Also, in the major release version the ligands are stripped out. Is this a bug? If not, I would like to request that the ligands be left in the structures. Thanks so much Kendall

2 1

The individual site refinement for Low resolution data (~3.8A)
by Zhang yu 14 Apr '11

14 Apr '11

Dear phenixer, Phenix suggested "Individual site" refinement is only suitable for high or midi resolution data (<3.5A). What is the alternate strategy to refine the atom coordinates of low resolution data? Yu

5 17

occupancy refinement when alternate conformers clash
by Kendall Nettles 13 Apr '11

13 Apr '11

Hi, I am refining an RNA structure where on set of base pairs has alternate conformers, and the B alternates from the paired bases clash. That is, the structure should be viewed as A alternate in one base paired with B alternate in the other base. The refinement blew both B alts out of the density to prevent their clash. How can I fix this? Thanks for your help, Kendall Nettles

2 1

O-linked glycosylation refinement in Phenix
by Qiang Chen 12 Apr '11

12 Apr '11

Dear all, I'm refining a structure which has both N-linked and O-linked glycosylation. I use Phenix to do the refinement. It works well for the N-linked NAG. I defined the link as the following: apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid 701" residue_selection_2 = "chain A and resname ASN and resid 518" } But it doesn't work when I defined the fucose-threonine link as the similar way: apply_cif_link { data_link = "FUC-THR" residue_selection_1 = "chain A and resname FUC and resid 801" residue_selection_2 = "chain A and resname THR and resid 596" } The error message is "missing CIF link: data_link_FUC-THR". Does anyone have the cif link file of FUC-THR? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

4 5

(Anisotropic ADP vs. isotropic ADP) coupling with occupancy refinement
by Young-Jin Cho 12 Apr '11

12 Apr '11

Dear phenix developer and users, I am just wondering while I was taking a small molecule X-ray course. I used to run refinement with anisotropic ADP when it is high resolution about better than 1.5 or 1.6 A. My question is when you do this with occupancy refinement, does phenix.refine take care the alternative conformations with aniostropic ADP (I guess so) even at low occupancy? Due to lack of electrons (scattering factor), I experienced that small molecule refinement applies Anisotropic ADP for the atoms (about more than 2 e- in occupancy) while applying isotropic ADP for the less occupied atoms (in an alternative conformation). Would it help if we apply this method to our macro molecular system when you have residues that have low occupied alternative residues? Is so, could we have something like script or else either to modify a pdb file or to make this in consideration during refinement? Any information or comments are welcome. Thanks in advance, Young-Jin

2 1

help me to install phenix on ubuntu10.4
by 王瑞 11 Apr '11

11 Apr '11

Excuse me,I'm a freshman ,could anyone tell me how to install phenix on ubuntu10.4? I have download phenix-installer-1.7-650- intel-linux-2.6-x86_64-fc12.tar.gz. when I install it in terminal,there was a error notice:"./install:no such file or directory"!Could anyone help me? Many thanks!

2 1

phenix don't start
by albert 10 Apr '11

10 Apr '11

Dear: I installed Phenix-1.7-650 in my SUSE Linux Enterprise 10 SP3 X64 system from source code. When I source /soft/phenix-1.7/phenix-1.7-650/phenix_env and try to run it by typing phenix in terminal, it is said: Traceback (most recent call last): File "/soft/phenix-1.7/phenix-1.7-650/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/soft/phenix-1.7/phenix-1.7-650/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/soft/phenix-1.7/phenix-1.7-650/phenix/wxGUI2/App.py", line 11, in <module> import wx ImportError: No module named wx The python in my OS is 2.4 with wxpython installed. I don't know why it cannot start. could you please give me some advices? THX

2 1

secondary structure restraints
by Panne Daniel 08 Apr '11

08 Apr '11

I am having problems with the secondary structure restraints in phenix.refine (1.6.4-486). I wrote a ss restraints file and use this as an input file. In the log file I can see that the file is read but the atom selections used by phenix.refine do not correspond to those set in the restraints file. I have turned off automatic ss detection. Any advice? Thanks, Daniel

3 3

difficulties with the refinement of a Cadmium containing pdb file
by Vellieux Frederic 08 Apr '11

08 Apr '11

Hi all, I have some difficulties refining (what happens is an error status, i.e. no refinement taking place) of a coordinate file that contains Cadmium ions. The person here who has already refined a structure containing Cd ions using Phenix is not here at the moment (otherwise I would have asked him). In case you wonder: the CD is shifted 1 position to the left as is required for metal ions in a PDB. Phenix choked. So I ran ReadySet on the input pdb file and gave the output file to Phenix for the next attempt. Still failed, and the error message I get is: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the PDB file to resolve the problem and/or supply a Cif file with matching restraints definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix_ready_set and phenix.elbow are available for creating restraints definitions (CIF files). Running phenix.elbow (phenix.elbow input_file.pdb --do-all) does not seem to do anything - no output file seems to be generated. Hence I am quite at loss here. Ready Set (from the gui) generated a file called name_of_the_coordinate_file.metal.edits , which is used by phenix for the next attempt but which does not seem to solve the problem. Thanks for any advice, Fred.

2 3

Re: [phenixbb] How to define link in phenix (rna3p) ?
by Ralf W. Grosse-Kunstleve 07 Apr '11

07 Apr '11

> Hi. I came across with the following post when I was dealing with a > similar issue (adding a modified nucleotide to RNA). I could create > .cif using elbow/reel as well, but I was wondering where to define > the link type between residues in phenix. You can use the apply_cif_link parameters. > For RNA, I typically see "rna3p', but with my newly created residue > linked to normal oligo, the link is formed, but recognized as Link ID > 'p'. Also, the newly created molecule is recognized as 'peptide', > although I defined _chem_comp.group in .cif file as RNA. The _chem_comp.group value is ignored by phenix.refine. The classifications are obtained via analysis of the atom names and the bonding in the monomer definitions. >------------------------------------------ >Chain: "Q1" > Number of atoms: 74 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 3, 74 > Classifications: {'RNA': 2, 'peptide': 1} > Modifications used: {'5*END': 1, 'rna3p': 2} > Link IDs: {'p': 1, 'rna3p': 1} >------------------------------------------ It is strange that it thinks there is a peptide but still applies two rna/dna links. Could you send me (not the list) the part from the pdb file with the Q1 chain? Ralf

1 0

CUA Ligand issue
by Bradley Hintze 07 Apr '11

07 Apr '11

Hello, I am trying to refine PDB 1YEW using the default phenix settings. $phenix.refine 1yew.pdb 1yew.mtz yields: ''' Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 6 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. ''' $ phenix.ready_set 1YEW_H.pdb yields: ''' Sorry: Atoms in the input are supposed to be bound CU1(CUA) - CU2(CUA) = 2.58 Fix the input file and retry ''' I assume this means that the Cu atoms in CUA are at an inappropriate distance. Is there an easy way to find out what the appropriate distance is? Can I fix this in coot? Thanks, Bradley

2 1

How to define link in phenix (rna3p) ?
by Maehigashi, Tatsuya 07 Apr '11

07 Apr '11

Hi. I came across with the following post when I was dealing with a similar issue (adding a modified nucleotide to RNA). I could create .cif using elbow/reel as well, but I was wondering where to define the link type between residues in phenix. For RNA, I typically see "rna3p', but with my newly created residue linked to normal oligo, the link is formed, but recognized as Link ID 'p'. Also, the newly created molecule is recognized as 'peptide', although I defined _chem_comp.group in .cif file as RNA. ------------------------------------------ Chain: "Q1" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Classifications: {'RNA': 2, 'peptide': 1} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'p': 1, 'rna3p': 1} ------------------------------------------ Any input will be appreciated. Sincerely, "T" On Wed, Nov 17, 2010 at 7:43 AM, Gerwald Jogl <Gerwald_Jogl at brown.edu<http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: > Hi All, > > I am refining several modified nucleotides in ribosomal RNA > (N2-methyl-guanosine and similar). While the restraints generation with > phenix.reel work quite well, I am unable to get the phosphate oxygen > restraints applied properly. Phenix.refine recognizes the links but for some > reason the phosphate groups come out quite distorted... > > For example, angles after refinement: > O3 (1) - P (2, modified) - OP2 (2) = 80 deg and > O3 (1) - P (2, modified) - OP1 (2) = 127 deg > > > Here is part of the phenix.refine log on reading the coordinates: > > Chain: "A" > Number of atoms: 32526 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 1513, 32526 > Unusual residues: {'MA6%rna3p': 2, '5MC%rna3p': 3, '5MC%rna2p': 1, > '7M > G%rna3p': 1, '2MG%rna3p': 1, 'UR3%rna2p': 1, 'M2G%rna3p': 1, '4OC%rna3p': 1} > Classifications: {'undetermined': 11, 'RNA': 1502} > Modifications used: {'5*END': 1, 'rna3p': 1318, 'rna2p': 195} > Link IDs: {'rna3p': 1318, 'rna2p': 194} > Chain breaks: 1 > > I am at a loss about how to fix this as all links and restraints seem to be > in place. > > Many thanks for advice, > Gerwald ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Re: [phenixbb] B-factors vs resolution
by miket＠chem.ucla.edu 07 Apr '11

07 Apr '11

Usually one will describe ordered parts of a protein vs disordered parts based on B factors. Is the higher resolution protein more ordered and that may have contributed to its stronger diffraction? -- Are the two crystals with different max resolution isomorphous? B-factors contain contributions from both dynamic and static disorder. Your difference in b-factors and resolution are both likely due to the fact that your higher-resolution data comes from a more ordered crystal, not a less dynamic protein. More ordered crystals diffract better, but if the two crystals were grown in the same conditions and the crystals are isomorphous I doubt that there is any difference in the dynamics of the molecules. If you are interested in which parts of your protein are more dynamically disordered you may want to consider (within a single dataset) which atoms have high b-factors relative to the average b-factor for all the atoms in that dataset. 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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tools to obtain ADP?
by Jason 07 Apr '11

07 Apr '11

Hi, Is there a convenient tool to obtain ADP for each chain or ligand or a selective group? phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Question about anisotropic refinement
by Louis Lazar 07 Apr '11

07 Apr '11

I have several structures that I am refining (~1.05A), and I have a question about anisotropic refinement. I have read a couple things about whether or not to refine waters anisotropically, as opposed to hydrogen, which I never refine anisotropoically. I am wondering what the general consensus is on it, and if anyone has anything from the archives (I'm having trouble searching through) or papers that I should read, please don't hesitate to let me see them. Thanks very much in advance Regards, Louis

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Ligand conformations.
by Yuri 06 Apr '11

06 Apr '11

Has anyone ever reported seeing 2 different binding confromations for a ligand that was soaked vs. the same ligand co-crystallized? -- Yuri Pompeu

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How to fix c-beta deviation?
by Jason 06 Apr '11

06 Apr '11

Hi, I have tried to regularize my protein structure in coot and use ramachandran restrain to improve statistics (and then release them). However, I can not make the c-beta deviation be zero. Is there some special way to improve c-beta deviation? Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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B-factors vs resolution
by Yuri 06 Apr '11

06 Apr '11

I am refining a 1.3 A structure the maps look great and I notice the main chain B factors are all around 7~12. I have refined the same enzyme at resolution 2.2 A and the B factors here were around 25~30. The question that comes to mind is: Usually one will describe ordered parts of a protein vs disordered parts based on B factors. Is the higher resolution protein more ordered and that may have contributed to its stronger diffraction? Or are the B factors values artifacts of refinement? -- Yuri Pompeu

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why are my B factors being "refined"
by Scott Classen 06 Apr '11

06 Apr '11

Hello Phenix community, I'm currently using nightly build 718, but this behavior is exhibited since sometime in the 1.6.xx releases too. I've turned off ADP refinement (only doing rigid_body refinement) and set the b_iso specifically as such: modify_start_model { selection = None adp { atom_selection = None randomize = None set_b_iso = 55 convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None } Yet the output PDB file has all b-factors in the 100s. Whazzup with that? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Modeling Disordered Domains
by Damian Ekiert 06 Apr '11

06 Apr '11

Perhaps inspired by the fierce debate on this BB and elsewhere about how to model disordered side chains, I would like to present the following scenario (my current refinement project): The structure was solved by molecular replacement, is 3.25Å resolution, and ~70% solvent. I have 6 copies of a large complex in the AU (~100kDa per protomer). Only one copy is fully ordered. In the other 5 copies, a entire domain (~25kDa) is largely disordered (some have patchy residual density, but not readily interpretable). Altogether, this means that I am missing ~20% of the total protein in the AU. It seems that how you model this much "missing" material could have a significant effect on the final refined model. This is something we have observed a number of times, so I am wondering if anyone can suggest ways to deal with this aside from just leaving the domains out entirely. In this case, the missing domain is connected by two short hinges that restrict the rotational degrees of freedom considerably (you can think of the missing domains as a door--it can only pivot about the hinge, can't be flipped upside-down or sideways, etc., and is anchored close to the door frame). Additionally, crystal packing and steric constraints restrict the "sweep" of the missing domains to further pinpoint their location. Is it worth trying to model this? My impression from some earlier posts was that most people were content for disordered regions to be modeled as bulk solvent (rather than fiddling with masks to also cover the expected location of protein, etc.), but I wonder if you may actually substantially improve the model when this much protein is disordered. I guess I am imagining something analogous to a rigid body fit to the mean position of the disordered domains and a TLS-like ADP description of the motion (with a very large magnitude to account for the large displacement), but I am open to suggestions. On a final note, regarding those pesky missing side chains: any thoughts on trying to employ a "Ringer"-like approach to model some of these (Fraser, et al., Nature 2009, 462(7273):669-673)? Is this practical (maybe this would add to many additional parameters)? Best, Damian Ekiert

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Re: [phenixbb] occupancy on a special position
by Maia Cherney 06 Apr '11

06 Apr '11

Hi, I have a water on a two fold axis, I gave it occupancy 0.50, but the program makes it 1.0. I know this was discussed before, but we have to abide by the PDB rules, that is to have this occupancy =0.5. Could you please, fix this problem. Maia

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Question about structure quality
by Jason 06 Apr '11

06 Apr '11

Hi, I have a refined structure with phenix. The resolution=3.8 angstrom. Molprobity analysis shows following. Can anyone tell me if the structure is acceptable or I need to do something to improve it before going to publication? Thanks. Poor rotamers20.95%Goal: <1%Ramachandran outliers6.15%Goal: <0.2%Ramachandran favored80.13%Goal: >98%Cβ deviations >0.25Å23Goal: 0Residues with bad bonds: 0.00%Goal: 0%Residues with bad angles:0.75% -- ====================== Jason Structural Biology Department University of Pittsburgh ======================

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