- phenixbb - phenix-online.org

on the eff file
by Smith Liu 20 Mar '15

20 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) 19 Mar '15

19 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 19 Mar '15

19 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 19 Mar '15

19 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) 15 Mar '15

15 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 09 Mar '15

09 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 06 Mar '15

06 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 26 Feb '15

26 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 26 Feb '15

26 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 26 Feb '15

26 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 26 Feb '15

26 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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on TLS for Phenix refine
by Smith Lee 23 Feb '15

23 Feb '15

Dear All, For TLS, the document says, "Can I use both TLS and anisotropic ADPs? Yes, but not for the same atoms - since TLS is essentially constrained anisotropic refinement, the two methods are mutually exclusive". In the "Refinment settings" of the Phenix refine graphical interface, will you please tell me which button is for the anisotropic ADP? The individual B-factors, or the Group B-factors, or only the "Optimize X-ray/ADP weight"? I am looking forward to getting your reply. Smith

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Odd behaviour of real-space refinement
by Tristan Croll 22 Feb '15

22 Feb '15

Hi all, I'm just finalising the re-refinement of a 3.6 Angstrom structure. The stats in general are excellent (Rwork/Rfree = 0.219/0.260; Ramachandran outliers 0.12%; Clashscore < 2; rotamer outliers 2.1%) and I've gone through the whole structure to check and double-check fit to the density. I'm very confident that it's effectively correct. When I run through a fairly standard refinement protocol (XYZ coords, Individual B-factors, optimizing weights, secondary structure restraints), all seems fine - the Rfree rattles around within 0.2% or so. But when I include the real-space refinement option, very strange things start to happen. Each rsrl step causes a 3-4% jump in both Rwork and Rfree, and jumps the Clashscore up to 40 or so. Rotamer outliers briefly go to zero but then increase substantially (to 6+%) in subsequent steps, and the number of Ramachandran outliers increases. I thought I'd missed some dreadful error in my structure until I looked more closely at the results. Some very nonsensical changes have been made - for example, an arginine in the middle of a beta-sheet (admittedly with no observable density associated with its sidechain, but register is well determined by surrounding residues and backbone density is clear) was flipped from its original orientation to point directly into the hydrophobic core of the domain. Somewhat surprising, to say the least. Is this a bug in the algorithm, or is it simply that 3.6A is too low resolution for it to work reliably? My version of Phenix is a nightly build from about 2 weeks ago. Happy to share coordinates and log files if necessary. Thanks, Tristan

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Odd behaviour of real-space refinement
by Tristan Croll 21 Feb '15

21 Feb '15

Hi all, I'm just finalising the re-refinement of a 3.6 Angstrom structure. The stats in general are excellent (Rwork/Rfree = 0.219/0.260; Ramachandran outliers 0.12%; Clashscore < 2) and I've gone through the whole structure to check and double-check fit to the density. The only stat that bugs me a little is the rotamer outliers (2.3%). When I run through a fairly standard refinement protocol (XYZ coords, Individual B-factors, optimizing weights, secondary structure restraints), all seems fine - the Rfree rattles around within 0.2% or so. But when I include the real-space option, very strange things start to happen. Each rsrl step causes a 3-4% jump in both Rwork and Rfree, and jumps the Clashscore up to 40 or so. Rotamer outliers briefly go to zero but then increase substantially in subsequent steps, and the number of Ramachandran outliers increases. I thought I'd missed some dreadful error in my structure until I looked more closely at the results. The attached image is an example of what's happened: an exposed arginine in the middle of a beta-sheet (admittedly with no observable density associated with its sidechain, but register is well fixed by surrounding residues) has been flipped from its original orientation (yellow) to point directly into the hydrophobic core of the domain. Somewhat surprising, to say the least. Is this a bug in the algorithm, or is it simply that 3.6A is too low resolution for it to work reliably? My version of Phenix is a nightly build from about 2 weeks ago. Thanks, Tristan

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Re: [phenixbb] Autobuild iterative omit map error
by Terwilliger, Thomas Charles 21 Feb '15

21 Feb '15

Hi Emily, (Back on-list so others can see the answer.) It seems that your PDB file has a "TER" record between residues ASN 446 and ALA 447 of chain B. Our parsing system interprets that as the end of chain B and thinks that ALA 447 is another chain. You can see this by running: phenix.print_sequence xxxxx.pdb I tried deleting the TER record and it looks as though autobuild will get past the interpretation stage with it taken out. Let me know if that doesn't do it! (Also...do you know why the TER record might be there? It is a little surprising!) All the best, Tom T On Feb 20, 2015, at 9:10 AM, Emilia C. Arturo (Emily) wrote: Thank you Tom! Attached are the reflections file, sequence file, input model pdb file, and the log file from phenix. Emily. On Fri, Feb 20, 2015 at 11:01 AM, Terwilliger, Thomas Charles <terwilliger(a)lanl.gov<mailto:[email protected]>> wrote: Hi Emily, I'm sorry for the trouble! I'll be happy to try and help with it. If you send me (off-list) the input files you are using and the full log file I'll have a look. All the best, Tom T On Feb 20, 2015, at 7:53 AM, Emilia C. Arturo (Emily) wrote: > Hello. > > I'd like to use phenix's Autobuild iterative omit map tool, but have run into an error I could use some help with. When the process aborts, the message that phenix outputs is that the input file has duplicate chains. I looked at the pdb file and I do not see duplicate chains; could the ANISOU records for each atom generated by TLS refinement be hanging up the process? I had no error with Autobuild when I started the iterative map process using an input file that had been generated by phenix.refine using the same configuration as the TLS refinement had used (except, of course, for the TLS parameters). > > Thanks for your attention. > Emily. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> <AutoBuild_run_85_1.log><III-40-C2_justscan3_xscale_cutresto29.mtz><PAH.fa><PAH_C2_ref22plus_refine_84.pdb>

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Autobuild iterative omit map error
by Emilia C. Arturo (Emily) 21 Feb '15

21 Feb '15

Hello. I'd like to use phenix's Autobuild iterative omit map tool, but have run into an error I could use some help with. When the process aborts, the message that phenix outputs is that the input file has duplicate chains. I looked at the pdb file and I do not see duplicate chains; could the ANISOU records for each atom generated by TLS refinement be hanging up the process? I had no error with Autobuild when I started the iterative map process using an input file that had been generated by phenix.refine using the same configuration as the TLS refinement had used (except, of course, for the TLS parameters). Thanks for your attention. Emily.

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on Bulk-solvent and scaling
by Smith Lee 20 Feb '15

20 Feb '15

Dear All, Will you please introduce to me briefly on the function of the step of Bulk-solvent and scaling in the Phenix refine and what is the corresponding mechanism? Smith

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On Phenix refinement
by Smith Liu 20 Feb '15

20 Feb '15

Dear All, The default number of cycles for the Phenix refinement graphical interface is 3 (should be macro-cycles). I have done a refinement with 3 default cycles, and I get the acceptable refinement results. Then I kept everything same, except I changed the cycles of refinement from 3 to 5, however the refinement result was ugly which was unacceptable (Rfree increased). The Phenix document regards 5 macrocycles refine is fine. For my situation, do you think the 3 macrocycles refine result is acceptable or not? If not acceptable, what do you suggest for improvement? I am looking forward to getting your reply. Smith

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erraser for DNA?
by Phoebe A. Rice 20 Feb '15

20 Feb '15

I know phenix has lovely DNA restraints, but I think the backbone of my lowish-resolution DNA structure could use more help. Is there anything like erraser for DNA that will make my DNA backbone as B-like as possible? ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago PRice(a)uchicago.edu<mailto:[email protected]>

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The discrepancy for determination of Ramachandran outliers by Coot and MolProbity
by Smith Lee 19 Feb '15

19 Feb '15

Dear All, It often finds for the Ramachandran favored determined by Coot, MolProbity regards as Ramachandran outliers. There are earlier posts regards Coot and MolProbity has different database for the determination of the Ramachandran plots. Then will you please let me know the correct way to correct the Ramachandran outliers by Coot in order to meet the MolProbity Standards? I am looking forward to getting your reply. Smith

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SA (torsion angle) along with B factor reset to low value.
by Tarek DawoD 19 Feb '15

19 Feb '15

to remove memory of the old original R-free flags (which is not available) and using a new test set, i reset the B factor and use SA (torsion angle) i got this error: not implemented: support of different sites. individual and sites.torsion_angles selection. what does that mean? thank you in advance TK_DawoD

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on HIS ** both conformations clash in the flipping
by Smith Lee 18 Feb '15

18 Feb '15

Dear All, In the log output of the Phenix refine, for the flipping of the N/Q/H residues before XYZ refinement, it often occurs something like "HIS ** both conformations clash, **PLEASE CHECK MANUALLY**". Will you please tell me what will clash with 1 of the 2 conformations of the specified HIS? I have checked the specified HIS in Coot, and I still do not know what does it mean for "both conformations clash". I am looking forward to getting a reply from you for clarification. Smith

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Computational Crystallography Newsletter - Volume 6, Number 1
by Nigel Moriarty 18 Feb '15

18 Feb '15

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2015 Articles Improved Probabilistic Estimates of Biocrystal Solvent Content Rapid evaluation of non-bonded overlaps in atomic models Short Communications Plan a SAD experiment, scale SAD data, and analyze your anomalous signal Validation of carbohydrate structures in CCP4 6.5 Disulfide bond restraints Fitting Tip #9: Avoiding excess cis peptides at low resolution or high B FAQ - Tips for coordinated metal refinement Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Quick request for addition to the line at the end of all these mails
by Morten Grøftehauge 17 Feb '15

17 Feb '15

Dear administrators of this list, Could you please add a line at the very end of these mails with: To unsubscribe click: www.somelink.com As it is it seems that some people have trouble getting off the list after they sign up. Because my spam filter keeps sending phenixbb mails into the spam folder. Which is likely because someone out there keeps flagging them as spam. If there's a link like that then gmail will even offer to attempt to unsubscribe for you. Just a thought. Cheers, Morten

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Please comment on the twinning analysis of my data by Xtriage
by Smith Liu 16 Feb '15

16 Feb '15

Dear All, I have done a Xtriage twinning analysis on my data. I summarize the result as following, Twinning analysis summary: The results of the L-test indicate that the intensity statistics below as expected. No twinning is suspected. Multivariate Z score L-test: 1.625. It further shows, Possible twin operators o merohedral twin operator(s) found, 1 pseudo-merohedral twin operator(s) found. Type Axis R metric(%) delta(le Pa) delta (lebed) Twin law PM 2-fold 4.934 2.547 0.036 l -k h Based on the above information, will you please advise me whether I need to input "l -k h" in the "Twin law" in "Other options" in "Refinement settings" in the Phenix refine graphical interface? I am looking forward to getting your reply. Smith

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On the cycles of the Phenix refinement
by Smith Lee 15 Feb '15

15 Feb '15

Dear All, The default number of cycles for the Phenix refinement graphical interface is 3 (should be macro-cycles). I have done a refinement with 3 default cycles, and I get the acceptable refinement results. Then I kept everything same, except I changed the cycles of refinement from 3 to 5, however the refinement result was ugly which was unacceptable. Someone told me once I have corrected the outliers by Coot, I can have a Phenix refinement with macro-cycles as 1, in order to avoid the Ramachandran corrected ones changing backing to Ramachandran outliers (Will you please further comment whether this strategy to correct Ramachandran outliers is acceptable or not). Thus can we regard the macro-cycles of Phenix refinement as one parameter for the refinement? And why the macro-cycles of the refinement can affect the refinement result? I am looking forward to getting your reply. Smith

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Re: [phenixbb] Fw: Fw: Question related to Phenix refinement
by Pavel Afonine 15 Feb '15

15 Feb '15

> From the attached the image, on the x-axis you can see the 4' rsrg and > 5'rsrg. > > I am looking forward to getting an explanation from you. Dear Smith, hope this will lead you to the answer: chevy:/net/chevy/raid1/afonine/sources % which fifig fifig: aliased to libtbx.find_files -g chevy:/net/chevy/raid1/afonine/sources % fifig rsrg ./cctbx_project/mmtbx/refinement/print_statistics.py: "realsrg" : "rsrg", chevy:/net/chevy/raid1/afonine/sources % All the best, Pavel

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Question related to Phenix refinement
by Smith Lee 15 Feb '15

15 Feb '15

Dear All. In the Phenix refine "run status" window, with the progression of the refinement, it occurs 3' bss, 3' rsrl, 3' xyz, 3' adp (for 3rd round of refinement). I guess xyz means the strategy is for x, y, z coordinates? Then what do bss, rsrl and adp mean? I am looking forward to getting your reply. Smith

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Test
by Paul Adams 15 Feb '15

15 Feb '15

-- 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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Hydrogen adding and real space refinement
by Smith Lee 13 Feb '15

13 Feb '15

Dear All, I find when I add H in the PDB file, in a refinement by Phenix, there is no real space refinement step (rsrl). If I do not add H in the PDB file, there is the rsrl step in the refinement. Somebody told me it was because there was a bug in the Phenix I downloaded, somebody told me if H added, there would be no real space refinement. I myself cannot clarify it by reading documents. Will you please clarify whether no rsrl step after H addition was because of bug or because of H addition leading to no rsrl step? And why H addition can lead to no rsrl step? I am looking forward to getting your reply. Best regards. Smith

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How should we estimate the "uncertainty" of the occupancy of an atom?
by Masaki UNNO 13 Feb '15

13 Feb '15

Hello We determined the structure of an enzyme-substrate complex. The substrate of the enzyme contains some partially occupied atoms. We were able to calculate the occupancies of these atoms using PHENIX_refine. By the way, I would like to know the uncertainties of the occupancies of these atoms. How can I estimate the uncertainties? For example, the occupancy of an atom was calculated as 0.65; can we write it as 0.65 (+/- 0.05) or 0.65 (+/- 0.1)? I know that it is related to B-factor and depends on the resolution (number of diffraction data per parameters), but I would like to know how to estimate (calculate?) the uncertainty. Could someone tell me about this issue? Best regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Masaki UNNO Graduate School of Science and Engineering Ibaraki University, JAPAN 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan Tel&Fax +81-294-38-5041 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [phenixbb] How should we estimate the "uncertainty" of the occupancy of an atom?
by Dale Tronrud 12 Feb '15

12 Feb '15

On 2/11/2015 12:34 PM, Keller, Jacob wrote: >> If your interpretation of your model depends on whether the occupancy of this atom is 0.65 or 0.75 crystallography is the tool you need. > > Did you mean *not* the tool...? > > JPK > You are right. I meant crystallography is NOT your tool. Sorry. Dale Tronrud

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Specifying Multiple Twin Operators
by Keller, Jacob 12 Feb '15

12 Feb '15

Dear List, Is it possible to specify multiple twin operators in Phenix? I have tetartohedrally-twinned data. If so, what's the syntax, and an example? And can it be done through the GUI? Thanks, Jacob ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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Question on Torsion-angle NCS
by Smith Liu 12 Feb '15

12 Feb '15

Dear All, For the graphical Phenix refine, if we click the "NCS options" button, a small window will occur. In the small window, will you please tell me how much should I input for "Weigh on NCS-related B-factor restraints"? I am looking forward to getting your reply. Smith

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Calculating map with electron scattering factors
by Omar Davulcu 11 Feb '15

11 Feb '15

Hi, everyone. Probably a silly question, but here goes... I'm trying to calculate a simulated map around a set of coordinates using the electron scattering table. Phenix.maps doesn't appear to allow selection of that particular scattering table. I noticed that phenix.refine allows me to select that table and I thought I would set the number of macro cycles to 0 and turn off all the refinement options and produce a map that way. I thought I would generate the structure factors needed as input with phenix.fmodel, but that also doesn't allow selection of the electron scattering table. So, my (naïve) question is: what am I doing wrong? Is there a way I can calculate this map in phenix? Any help would be greatly appreciated. Thanks much! Omar Davulcu

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on XYZ individual (reciprocal space) refinement
by Dialing Pretty 11 Feb '15

11 Feb '15

Dear All, Will you please tell me the XYZ individual (reciprocal space) refinement is executed by which strategy of the Phnix refinement? By XYZ coordinates, or by Optimize X-ray/ADP weight,or by Optimize X-ray/sterochemistry weight? Dialing

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on my Phenix refinment
by Smith Lee 10 Feb '15

10 Feb '15

Dear All, I have started a Phenix refinement, my strategy including xyz coordinates, real space, individual B-factors, Group B-factors, TLS parameters, Occupancies, optimize X-ray/sterochemistry weight, NCS restraints, and Automatically correct N/Q/H errors. Number of cycles is 3. It is now at the 3' bss stage. But will you please tell me why there is no rsrl stage occurred in the Run Status window (here I mean there is no 1' rsrl stage and 2' rsrl stage) even now it has reached the 3' bss stage? I am looking forward to getting your reply. Smith

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Global metrics for Ramachandran quality beyond %outliers?
by Shane Caldwell 09 Feb '15

09 Feb '15

I'm making a new thread because it's off the topic, but I have a question in response to this point <http://phenix-online.org/pipermail/phenixbb/2015-February/021691.html>: > [Doggy structure improved, as shown by how] The Ramachandran plot tightened This is interesting to me - other than eyeballing the plot, are there any quantitative metrics of Ramachandran distribution quality? At low-res or when refining a bunch of structures side-by-side it could be an additional indicator of quality of the model, without requiring having to inspect the plot. Of course manual inspection is always important in the end, but in early stages a global measure of spread could help guide refinement. I've seen %outliers used for this purpose, but that ignores that while a residue can be "allowed" it can still be far from a statistically likely conformation. From what I've seen, some users only consult Ramachandran to tweak residues until they pop into the "allowed" regions and stop there, which isn't the same as globally improving the geometry. Interested to hear thoughts (or it it's already in use, pointing me in the right direction!), Shane Caldwell McGill University On Thu, Feb 5, 2015 at 5:06 AM, Andreas Förster <docandreas(a)gmail.com> wrote: > Dear Almudena, > > I promise not to make a habit of advertising other programs on the Phenix > mailing list, but just once I would like to encourage you (and the > community) to try all the tools at your disposal. > > Different refinement programs have different strength and weaknesses. > Secondary-structure restraints in Phenix are great for low-resolution data, > but so is jelly-body refinement in Refmac. A dodgy 3.2 Å structure I'm > currently working on was improved dramatically by Buster-TNT. The > Ramachandran plot tightened, and R free plunged by four percentage points. > > > Andreas > > > > On 05/02/2015 10:44, Almudena Ponce Salvatierra wrote: > >> Dear all, >> >> I am refining my structure (data at 3 A), with a model that is complete. >> However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read >> "Improved target weight optimization in phenix.refine" (In the >> computational crystallographic newsletter 2011) and what I understand is >> that just by marking the boxes "improve xray/stereochemistry weight" and >> "improve xray/adp weight" it should work... giving me the best possible >> Rfree. >> >> I'm refining individual coordinates, occupancies, b-factors (isotropic >> for all atoms), TLS, and using secondary structure restraints, automatic >> ligand linking and experimental phases restraints. Also, I chose this >> strategy because I have finished building the structure and according to >> some of the suggestions in "towards automated crystallographic structure >> refinement with phenix.refine". >> >> I am actually quite confused and don't know what to think... is it a >> matter of the weights? is it only that this is as good as it gets? >> >> Any suggestions and comments are welcome. >> >> Thanks a lot in advance, >> >> Best, >> >> Almudena >> -- >> Almudena Ponce-Salvatierra >> Macromolecular crystallography and Nucleic acid chemistry >> Max Planck Institute for Biophysical Chemistry >> Am Fassberg 11 37077 Göttingen >> Germany >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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