- phenixbb - phenix-online.org

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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