- phenixbb - phenix-online.org

fixing rotamers with coot
by Benoît Masquida 19 Mar '15

19 Mar '15

Dear all, I am using Coot 0.7.2 and phenix 1.9-1692 on Ubuntu 13.10 and I have the following error message when I try to regularize zone, edit Chi angles or fix rotamer outliers. Error message :"Refinement setup failure. Failed to find restraints for : 'residue list' " Apparently a cif dictionary is missing that should be output by phenix to be used by coot. Does anyone has any idea? Thanks in advance. Benoit --

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on Phenix refine
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Will you please tell me which strategy of Phenix refine is for reciprocal space refinement? In the log, I often see "XYZ individual (reciprocal space)", will you please let me know whether "XYZ individual (reciprocal space)" is caused by "XYZ coordinates" or by "Optimize X-ray/sterochemistry weight"? Smith

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on the eff file
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Someone told me from the refine eff file, I can know what is my strategy for my refinement. I have run 2 refines with the same input files, For one refine, in the graphical interface I have checked xyz-coordinates, Real-space, Individual B-factors, Occupanies, Optimize X-ray/sterochemistry weight, Automaticaly orrect N/Q/H erros. For the other refine, I only checked XYZcoordinates, Real-space and Autonomously correct N/Q/H errors. I have checked the eff files from the 2 diffrent refines, but I cannot find any diffrence in the eff file. Thus will you please tell me how to find the diffrence in the 2 eff files? Or my strategies for each refine was recorded in the other files? I am looking forward to getting your reply. Smith

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the command to open the *.eff file
by Smith Lee 19 Mar '15

19 Mar '15

Dear All, Will you please tell me the command to open the *.eff file? I want to get the stratgies for my refinement. Smith

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phenix.development.optimize_model
by Colin Levy 19 Mar '15

19 Mar '15

Hi, I am running a Phenix development installation (dev_1977) and used the phenix.development.optimize_model option on a project of mine refined at 1.9Å. The output has certainly improved the R factors but I was curious as the refined model which is a rather globular structure has been refined utilising 17 TLS groups and anisotropic B factors. In its current state of development, how robust are these refinement choices and on what basis are they being determined? They differ somewhat from what I might have invoked manually? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk On 12/03/2015 15:19, "phenixbb-request(a)phenix-online.org" <phenixbb-request(a)phenix-online.org> wrote: >Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb >or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > >You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of phenixbb digest..." > > >Today's Topics: > > 1. Announcement and call for abstracts: Structural > Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, > Croatia (Capitani Guido (PSI)) > 2. how to correct residuess with missing atoms (Smith Liu) > 3. Re: how to correct residuess with missing atoms (Joel Tyndall) > 4. RESOLVE density modification (Mark A Saper) > 5. Re: RESOLVE density modification (Terwilliger, Thomas Charles) > 6. Nitric Oxide metal.edits not working? (Yarrow Madrona) > 7. Re: Nitric Oxide metal.edits not working? (Edward A. Berry) > 8. Group B factor refinement not working for low resolution data (??) > 9. Re: Group B factor refinement not working for low resolution > data (Pavel Afonine) > 10. Re: Group B factor refinement not working for low resolution > data (Phoebe A. Rice) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 6 Mar 2015 13:29:51 +0000 >From: "Capitani Guido (PSI)" <guido.capitani(a)psi.ch> >To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> >Subject: [phenixbb] Announcement and call for abstracts: Structural > Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia >Message-ID: > <D324C9581FD3114280044EDC6357A3E51BCE66CD(a)MBX114.d.ethz.ch> >Content-Type: text/plain; charset="us-ascii" > >Dear Colleagues, > >The 29th European Crystallographic Meeting (ECM29), to be held on August >23-28 in Rovinj, Croatia, will feature a Structural Bioinformatics >microsymposium >(http://ecm29.ecanews.org/programme/microsymposia/#ms10). All structural >bioinformatics topics with relevance to macromolecular crystallography >are welcome. >Abstract submission (for oral or poster presentation) is available at >http://ecm29.ecanews.org/participate/abstract-submission/, with deadline >March 23. >The final program will encompass two 30-min talks from invited speakers, >three 20-min talks chosen from the submitted abstracts, and poster >presentations. >Looking forward to many interesting contributions; with best regards, > >Guido Capitani > > > >Dr. Guido Capitani >Paul Scherrer Institute >OFLC/110 >5232 Villigen PSI >Switzerland >guido.capitani(a)psi.ch >Tel. +41 56 310 47 22 >http://www.psi.ch/lbr/capitani_-guido >http://www.eppic-web.org > > > > > > >------------------------------ > >Message: 2 >Date: Sun, 8 Mar 2015 18:11:19 +0800 (CST) >From: "Smith Liu" <smith_liu123(a)163.com> >To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> >Subject: [phenixbb] how to correct residuess with missing atoms >Message-ID: <46870f8b.b136.14bf8de1901.Coremail.smith_liu123(a)163.com> >Content-Type: text/plain; charset="gbk" > >Dear All, > >Is any function of Phenix or some other software which can be used to >correct residuess with missing atoms in the PDB file? > >I am looking forward to getting your reply. > >Smith >

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Ramachandran results from Structure_comparison tool
by Emilia C. Arturo (Emily) 18 Mar '15

18 Mar '15

Hello, I've just run the Structure comparison tool for the first time using phenix 1.9-1692. All the results tabs--except the Ramachandran tab--have per-residue values throughout the length of the ~450-residue sequence; the Ramachandran tab has values only through residue 429. The sequence file included with the run contains 453 residues. Each of the pdb files input to the run have between 445 and 450 residues each. Throughout the length of each model, all models are 100% sequence-identical to each other and to the sequence file. Is it a known bug, that the Ramachandran values are not output for all the residues for which there are values in the other tabs? Emily Arturo Ph.D. program in Biochemistry, Drexel Univ College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA

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labelit compatibility with mosflm
by Ursula Schulze-Gahmen 18 Mar '15

18 Mar '15

I tried to use LABELIT for the first time. I am using the version that comes with Phenix-dev-1951 (automatically installed through sbgrid). The program found some promissing solutions, but ends with the error: mosflm versions after 7.1.0 not supported It also doesn't seem to know ALS beamline 8.3.1 Any suggestions how to deal with this? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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gridding of maps & coot
by Roger Martin 18 Mar '15

18 Mar '15

Hi, in making ccp4 formatted binary files readable by coot there are two *determine_gridding methods on the c++ side of cctbx ; *http://cctbx.sourceforge.net/current/c_plus_plus/namespacecctbx_1_1maptbx.html 1) template<typename IndexValueType>af::tiny< IndexValueType, 3 > determine_gridding (uctbx::unit_cell const &unit_cell, double d_min, double resolution_factor, af::tiny< IndexValueType, 3 > const &mandatory_factors=detail::one_one_one, IndexValueType max_prime=5, bool assert_shannon_sampling=true); 2) template<typename IndexValueType>af::tiny< IndexValueType, 3 > determine_gridding (uctbx::unit_cell const &unit_cell, double d_min, double resolution_factor, sgtbx::search_symmetry_flags const &symmetry_flags, sgtbx::space_group_type const &space_group_type, af::tiny< IndexValueType, 3 > const &mandatory_factors=detail::one_one_one, IndexValueType max_prime=5, bool assert_shannon_sampling=true); From the python side these get called within http://cctbx.sourceforge.net/current/python/cctbx.maptbx.html#crystal_gridd… __init__(self, unit_cell, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, space_group_info=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True, pre_determined_n_real=None); In phenix code it appears that only resolution_factor is ever set and internally then only the first determine_gridding method ever gets called. For numerous space groups these grid dimensions aren't compatible with symmetry operations and if symmetry operations are added to the ccp4 binary file coot has issues with asu (asymmetric unit) fitting to the grid. http://www.ccp4.ac.uk/html/maplib.html If the symmetry operator equations are skipped then coot will read as if the map is P 1 and not know the space group and asu's. symmetry_flags would have to be set to something non-None to call the second method. And if the second determine_gridding method(which is spacegroup aware) would be used, the grid dimensions are compatible with symmetry operators and coot reads and works with the asu's (and my own custom code is also happy). For all the maps produced from phenix.refine runs I've examined they have a space group number between 1 and 230, no symmetry operators included and grid dimensions from the first determine_gridding method. Now there are a number of space groups which have different axes chosen. For example 155 can be R=Rhombohedral http://img.chem.ucl.ac.uk/sgp/large/155az1.htm or H=Hexagonal http://img.chem.ucl.ac.uk/sgp/large/155bz1.htm axes. The symmetry operators identify which one or some systems prepend a number on the space group number such as 155 -> 1155. But coot (0.7 or 0.8.1) doesn't respond to that; only to the symmetry operators I suppose because the symmetry operators are the most trustworthy. The functionality is already in cctbx. Is there a reason the second determine_gridding method(spacegroup aware) is not used by phenix? And a reason symmetry operator equations are not added to the output ccp4 binary files? How should a ccp4 binary know the R or H axes of the space group? (according to its format http://www.ccp4.ac.uk/html/maplib.html) -Roger

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Abstract deadline April 15 for Intl Conf. on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology" & Early Bird Registration deadline March 31
by Terwilliger, Thomas Charles 15 Mar '15

15 Mar '15

Abstract deadline April 15 for Intl Conf. on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology" & Early Bird Registration deadline March 31 15-Mar-2015 Dear Colleagues, It's time to register for the International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology", which will be held on the campus of the Weizmann Institute of Science in Rehovot, Israel June 7-11, 2015! The Abstract deadline is April 15, 2015. This conference is intended to foster international collaboration and to provide an overview for the most recent developments in Structural Biology and Structural Genomics and future impacts on biology, medicine and disease. See the web site at: http://www.weizmann.ac.il/conferences/ICSG2015 and the poster at: https://www.dropbox.com/s/i1s3hsg7a0chqi2/ICSG2015_Poster.pdf?dl=0 The scientific topics to be covered in ICSG 2015 include: · Deep sequencing for modeling and refinement of macromolecular structures · Membrane protein structure and function using complementary methods · Technological advances in XFEL, Cryo-EM, NMR, SAXS, MS, MX and macromolecular complexes · Combining low and high resolution data and modeling for structural biology · Synergistic use of 3D structures and deep sequencing to realize personalized medicine · Protein design and deep sequencing · Cancer, antibiotic resistance and drug discovery In order to widen the opportunities for younger researchers, we have organized satellite workshops before ICSG 2015 (during the day on June 7, 2015). These include: · Cryo-EM developments for structural biology [Sponsored by FEI] · Approaches to the translation of deep sequencing data into three-dimensions [Ron Unger; Sponsored by Instruct] · PHENIX: Automated determination of molecular structures [Tom Terwilliger, Li-Wei Hung & Pavel Afonine] · HKL3000: From X-ray diffraction images to structure determination in minutes [Wladek Minor] · Protein expression and characterization workshop [Tamar Unger & Yoav Peleg] · Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure & Function [Jaime Prilusky & Joel L. Sussman] Five oral presentations will be chosen from the posters, and six poster prizes will be awarded, so be sure to submit your abstracts by April 15, 2015! Speakers include: Arie Admon (Haifa) Lucia Banci (Florence) Pamela J. Bjorkman (Pasadena) Samir K. Brahmachari (Delhi) Susan Buchanan (Bethesda) Martin Caffrey (Dublin) Keith Dunker (Indianapolis) Mark Gerstein (New Haven) Wayne Hendrickson (New York) Eran Hodis (Boston) Yvonne Jones (Oxford) Roger Kornberg (Stanford) Luhua Lai (Beijing) Michael Levitt (Stanford) Michal Linial (Jerusalem) Abraham Minsky (Rehovot) Ken Mok (Dublin) John Moult (Rockville) Nathan Nelson (Tel Aviv) Stefan Raunser (Dortmund) Monica Roth (Piscataway) Dinakar M. Salunke (Gurgaon) Eran Segal (Rehovot) Philipp Selenko (Berlin) Sachdev Sidhu (Toronto) Henry Sobell (Rochester) Rotem Sorek (Rehovot) Jan Steyaert (Brussels) Shamil Sunyaev (Boston) Dan Tawfik (Rehovot) Janet Thornton (Hinxton) The FEBS National Lecturer Gunnar von Heijne (Stockholm) Soichi Wakatsuki (Stanford) Shigeyuki Yokoyama (Yokohama) Ada Yonath (Rehovot) Mingjie Zhang (Hong Kong) We are looking forward to welcoming you to the Weizmann Institute in the June of 2015! Sincerely yours, ICSG 2015 Local Organizing Committee Joel L. Sussman, Gideon Schreiber, Tamar Unger and Israel Silman, Weizmann Institute ICSG 2015 International Program Committee Cheryl Arrowsmith, (Structural Genomics Consortium, Toronto) Lucia Banci, (University of Florence, Florence) Jacqui Beckmann, (Swiss Institute of Bioinformatics, Lausanne) Mark Gerstein, (Yale University, New Haven) Yvonne Jones, (University of Oxford, Oxford) Luhua Lai, (Peking University, Beijing) Katsumi Maenaka, (Hokkaido University, Sapporo) Gaetano Montelione, (Rutgers University, Piscataway) John Moult, (Institute for Bioscience and Biotechnology Research, Rockville) John Norvell, Maryland (Founding Director of the NIGMS Protein Structure Initiative) Dinakar Salunke, (Regional Centre for Biotechnology, Gurgaon) Gideon Schreiber, (Weizmann Institute, Rehovot, Israel) Joel L. Sussman, (Weizmann Institute, Rehovot, Israel) Janet Thornton, (European Bioinformatics Institute, Hinxton) Gunnar von Heijne, (Stockholm Bioinformatics Center, Stockholm) Ron Unger, (Bar-Ilan University, Ramat Gan) Shoshana Wodak (University of Toronto, Toronto) International Structural Genomics Organization Executive Committee Lucia Banci Aled Edwards Jennifer Martin Joel Sussman Tom Terwilliger Shigeyuki Yokoyama

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viewing ligand_identification output files
by Emilia C. Arturo (Emily) 14 Mar '15

14 Mar '15

Hello, I've recently used--for the first time--phenix's ligand_identification tool via the GUI, and am now examining the output files. I'm writing to ask for advice on how to view the map and models using Coot. I could open the 'model_RSR_FITTED_###.pdb' file with PyMOL, and I could inspect where in the model the fit ligand sits, but I prefer to look at the map using Coot. At this point I have two problems: First, when I Auto Open the resolve.mtz file in Coot, the model I'd input to ligand_identification is clearly not aligned with the map. What could have happened here? And how might I fix it? Second, the same 'model_RSR_FITTED_###.pdb' file I opened with PyMOL has in Coot just one chain, and that contains only the fit ligand. Thanks in advance for any input, Emily Arturo Ph.D. program in Biochemistry, Drexel Univ College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA

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Group B factor refinement not working for low resolution data
by 李翔 12 Mar '15

12 Mar '15

Hi, I am working on my ~6A data with molecular replacement method. The MR works out and after rigid body and xyz refinement the result is OK. However, when I tried the ADP refinement with Group B factor option in PHENIX GUI, the R factor significantly increased as well as the B-factor. Any expert can help me to take a look and give some suggestions please? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, University of Michigan Email：lixiang1642(a)gmail.com

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Nitric Oxide metal.edits not working?
by Yarrow Madrona 10 Mar '15

10 Mar '15

Hello, I am running phenix version 1.9-1692. I have restrains for a nitric oxide ligand that I have used previously to refine a heme iron-NO linked structure. I have pasted them below. For some reason. The NO always gets moved a little to far from the iron. Here is a coot screen shot: https://www.dropbox.com/s/85c1ad2kecwebij/coot.png?dl=0 Can someone please help me resolve this issue? Thank you. -Yarrow ---------------------------------------------------------------------------------- metal edits file: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name FE and chain A and resname FE and resseq 499 atom_selection_2 = name N and chain A and resname NMO and resseq 510 distance_ideal = 1.75 sigma = 0.1 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name FE and chain A and resname FE and resseq 499 atom_selection_2 = name N and chain A and resname NMO and resseq 510 atom_selection_3 = name O and chain A and resname NMO and resseq 510 angle_ideal = 160 sigma = 5 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name FE and chain B and resname FE and resseq 499 atom_selection_2 = name N and chain B and resname NMO and resseq 510 distance_ideal = 1.75 sigma = 0.1 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name FE and chain B and resname FE and resseq 499 atom_selection_2 = name N and chain B and resname NMO and resseq 510 atom_selection_3 = name O and chain B and resname NMO and resseq 510 angle_ideal = 160 sigma = 5 } } --------------------------------------------------------------------- CIF file # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level NMO NMO "nitric oxide " ligand 2 2 . # data_comp_NMO # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z NMO N N N . -0.1324 -0.0924 0.5896 NMO O O O . 0.1324 0.0924 -0.5896 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd NMO N O double 1.223 0.020 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd NMO plan-1 N 0.020 NMO plan-1 O 0.020

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RESOLVE density modification
by Mark A Saper 09 Mar '15

09 Mar '15

I am trying to run RESOLVE density modification with the output of a SAD Phaser run (dev-1965). There are 3 input files: high resolution/experimental F’s and I’s, map coefficients and phases, and sequence. I consistently get this error: … ******************************************************************************** Failed to carry out AutoBuild_set_up_build: For finding NCS from sites an MTZ file is required ******************************************************************************** I do not know which MTZ file is being referred to. I have tried entering NCS as blank, 1, or turning it off in the NCS… options panel. I also tried including the substructure PDB file. Any suggestions? -Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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how to correct residuess with missing atoms
by Smith Liu 08 Mar '15

08 Mar '15

Dear All, Is any function of Phenix or some other software which can be used to correct residuess with missing atoms in the PDB file? I am looking forward to getting your reply. Smith

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Announcement and call for abstracts: Structural Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia
by Capitani Guido (PSI) 06 Mar '15

06 Mar '15

Dear Colleagues, The 29th European Crystallographic Meeting (ECM29), to be held on August 23-28 in Rovinj, Croatia, will feature a Structural Bioinformatics microsymposium (http://ecm29.ecanews.org/programme/microsymposia/#ms10). All structural bioinformatics topics with relevance to macromolecular crystallography are welcome. Abstract submission (for oral or poster presentation) is available at http://ecm29.ecanews.org/participate/abstract-submission/, with deadline March 23. The final program will encompass two 30-min talks from invited speakers, three 20-min talks chosen from the submitted abstracts, and poster presentations. Looking forward to many interesting contributions; with best regards, Guido Capitani Dr. Guido Capitani Paul Scherrer Institute OFLC/110 5232 Villigen PSI Switzerland guido.capitani(a)psi.ch Tel. +41 56 310 47 22 http://www.psi.ch/lbr/capitani_-guido http://www.eppic-web.org

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Phenix mailing list and web server
by Paul Adams 06 Mar '15

06 Mar '15

Dear Phenix Mailing List Subscribers many of you will have noticed issues with the Phenix web site, bulletin board and help mail addresses over the last week. This was a result of a serious hardware failure. Today these services should all be back on line and functioning normally. If you encounter any problems please let us know. Many thanks for your patience. Cheers, Paul -- 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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Test
by Paul Adams 05 Mar '15

05 Mar '15

Test of restored Mailman system. Please ignore. -- 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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get_cc_mtz_pdb for neutron data table
by Maxime Cuypers 27 Feb '15

27 Feb '15

hi, i need the correlation coefficients map/residues for a publication, which command should i use to get phenix.get_cc_mtz_pdb to take into account the neutron scattering tables? seems it uses the x ray tables by default. i can not find it on this page: http://www.phenix-online.org/version_docs/1.8.3-1472/get_cc_mtz_pdb.htm#anc… many thanks for your reply. -- Dr. Maxime Cuypers

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hiding clash dots
by Sebastiano Pasqualato 26 Feb '15

26 Feb '15

Hi all, a quick question: how do I get rid of the clash dots that appear in Coot, when opened from a phenix job? thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>

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on phenix.cut_out_density
by Smith Lee 26 Feb '15

26 Feb '15

Dear All, Can the mtz file produced by phenix.cut_out_density be used by Phenix refine for refinement? Smith

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a sharp rise of R-free in resolution bin
by Singh, Bishal 25 Feb '15

25 Feb '15

Hello everyone, I am refining a structure at 2.3 A resolution. R-work/R-free is 26/31 and is not reducing further. When I looked into the resolution bin, I notices a sharp rise of R-free between resolution range 2.5-2.6 A (marked in figure below). However R-work is fine. I am doubtful of reducing the resolution to 2.5 A or lower. Please suggest me your opinion. Your words will be highly appreciated. With regards, Bishal Singh PhD Student University of Heidelberg, Germany

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How to define a disulfide bond between symmetry related molecules in phenix.refine
by Michael Hothorn 25 Feb '15

25 Feb '15

Dear all, I am trying to refine an intermolecular disulfide bond in phenix.refine. The disulfide involves Cys 188 in chain A and Cys 188 of chain B of a symmetry related molecule, with symop -X, Y+1/2, Z+1/2. There are two molecules in the AU, SG is P212121. I generated the following SSBOND entry in the pdb header: SSBOND 2 CYS A 188 CYS B 188 1555 3555 2.04 Based on this: http://www.wwpdb.org/documentation/file-format/format33/sect6.html the format seems fine, but the disulfide is not being recognized during refinement. Could someone point out to me how to correctly define this for phenix.refine. Thanks! Michael

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sharp rise of R-free in resolution bins
by Singh, Bishal 25 Feb '15

25 Feb '15

Hello everyone, I am refining a structure at 2.3 A resolution. R-work/R-free is 26/31 and is not reducing further. When I looked into the resolution bin, I notices a sharp rise of R-free between resolution range 2.5-2.6 A (marked in figure below). However R-work is fine. I am doubtful of reducing the resolution to 2.5 A or lower. Please suggest me your opinion. Your words will be highly appreciated. With regards, Bishal Singh PhD Student University of Heidelberg, Germany

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On Ramachandran restraints of Phenix refine
by Smith Lee 25 Feb '15

25 Feb '15

Dear All, If my resolution was between 2.5-3.0 A, and if I did not use Ramachandran restraints in the Phenix refine the Ramachandran outliers would be increased significantly during the refinement process, in this situation may I use Ramachandran restraints in the Phenix refine? I am looking forward to getting your reply. Smith

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Bug? phenix.hyss crashes on reading CNS def file
by Mark A Saper 24 Feb '15

24 Feb '15

I am trying the example described on this documentation page: http://www.phenix-online.org/download/documentation/cci_apps/hyss/examples.… For mbp.hkl the HySS command suggested is: phenix.hyss $CNS_SOLVE/doc/html/tutorial/data/mbp/mbp.hkl 4 yb —symmetry $CNS_SOLVE/doc/html/tutorial/data/mbp/def The software does not expect the “{“ character in the def file. I can send you the Traceback on request. I am running dev-1951. -Mark

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