- phenixbb - phenix-online.org

how to use a dimer as a search model by MRage
by fukamitka＠chugai-pharm.co.jp 09 Dec '14

09 Dec '14

Dear all, I have a dataset, there are 4 or 5 copies of two different hetero dimers (i.e. 4 different chains) in au, and I'd like to use the dimers as search models. I ran phenix.MRage with a phil file below, and it searched each chains separately, as expected. In this case, I want to search dimerA (containing chain1 and 2) and dimerB (chain3 and 4) as 2 search templates, but I couldn't find how to specify a dimer as a component. Using dimer.pdb and dimer.seq caused an error (sequence file can't contain multiple sequence). How do I write an input file? Regards, ------------------------- composition { count = 5 component { sequence = dimerA-chain1.seq stoichiometry = 1 template { pdb = dimerA-chain1.pdb } } component { sequence = dimerA-chain2.seq stoichiometry = 1 template { pdb = dimerA-chain2.pdb } } component { sequence = dimerB-chain3.seq stoichiometry = 1 template { pdb = dimerB-chain3.pdb } } component { sequence = dimerB-chain4.seq stoichiometry = 1 template { pdb = dimerB-chain4.pdb } } } ------------------------- ----- Takaaki Fukami (mailto:[email protected]) Discovery Research Dept. (Biostructure Gr.) Chugai Pharmaceutical Co.,Ltd.

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Re: [phenixbb] micro-beam?
by Edna Patricia Matta, Ms 08 Dec '14

08 Dec '14

Thanks everybody for the information, A good week to all, Edna Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 [http://www.med.mcgill.ca/nahum/images/tel.png] TEL: 1-514-398-7275 [http://www.med.mcgill.ca/nahum/images/fax.png] FAX: 1-514-398-1287 ________________________________ From: Jurgen Bosch [jbosch2(a)jhu.edu] Sent: Monday, December 08, 2014 11:47 AM To: Edna Patricia Matta, Ms Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] micro-beam? tiny is relative - for some tiny means 100 µm … APS has several beam line with 25 or 50 µm focus which are not considered microfiches but still small enough for most things. SSRL 12-2 would be another option 10µm ESRF 5µm (?) SLS 10 -50 µm Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu On Dec 8, 2014, at 11:40 AM, Edna Patricia Matta, Ms <edna.matta(a)mail.mcgill.ca<mailto:[email protected]>> wrote: Good morning everyone, I have very tiny protein crystals (verified) but I do not know what facility has micro-beam to shoot them, Any information that could help me? Thanks in advance, Best, Edna Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 TEL: 1-514-398-7275 FAX: 1-514-398-1287 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

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compiling phenix from source error
by Maxime Cuypers 08 Dec '14

08 Dec '14

hi all, am getting the following error installing phenix from source dev-1839. (tried with source from 1.9-1692 with same error) am on latest kubuntu. any idea on how to debug? -see below report... PS: am compiling from source because i need a minor modification of the neutron scattering table which requires compilation. cheerios, .... Installing Xrender... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log getting package xrender-0.8.3.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/xrender-0.8.3.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 507, in build_wxpython_dependencies_linux self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 385, in build_compiled_package_simple log=pkg_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 203, in configure_and_build self.call("./configure %s" % " ".join(list(config_args)), log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base"' failed with exit code 1 max@A7K:/pgmax/phenix-installer-dev-1839$ uname -a Linux A7K 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux -- Dr. Maxime Cuypers

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Announcement - NSLS-II Early-Science Workshop for NIH-funded beamlines
by Robert Sweet 08 Dec '14

08 Dec '14

Sent on behalf of the Workshop Organizing Committee The NIH-funded ABBIX structural biology beamlines at the NSLS-II are approaching completion, delivering two crystallography and one scattering beamline for biological sciences. The performance of these beamlines will present opportunities previously unattainable at synchrotron light sources, creating challenges for data collection and scientific discovery. The beamlines will provide a photon-beam flux density at least five orders of magnitude greater than that achievable at the NSLS, and orders of magnitude greater than that achievable today at any synchrotron light source. Participation in the first science undertaken at these beamlines represents a unique opportunity for scientists to help deliver on their potential. We are organizing a workshop at BNL, to occur on Jan. 28-29, 2015, to help define and develop further the priorities for the scientific commissioning of these beamlines and their entry into routine operation. Interested participants will be able to present and discuss their vision for the early science case for each beamline, thereby helping to shape the international scene for structural biology. Find workshop information at http://workshops.ps.bnl.gov/?w=ABBIXJan2015, including a draft agenda and an opportunity to register and submit an abstract.

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micro-beam?
by Edna Patricia Matta, Ms 08 Dec '14

08 Dec '14

Good morning everyone, I have very tiny protein crystals (verified) but I do not know what facility has micro-beam to shoot them, Any information that could help me? Thanks in advance, Best, Edna Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 TEL: 1-514-398-7275 FAX: 1-514-398-1287

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neighbouring residues with symmetry
by Swanand Gore 08 Dec '14

08 Dec '14

Hi All, I am sure this has been asked and answered a lot of times... Is there a python script somewhere that reads a mmcif file and for any residue in it, returns a list of residues within a certain distance of it. And it returns any symmetry-related copies of residues too within that distance. Any pointer greatly appreciated. Thanks, Swanand -- Swanand Gore, wwPDB at PDBe-EMBL-EBI, Cambridge swanand(a)ebi.ac.uk ............. http://pdbe.org

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Institut Pasteur/CCP4 Joint Macromolecular Crystallography School "From data processing to structure refinement and beyond"
by Alejandro Buschiazzo 06 Dec '14

06 Dec '14

Dear colleagues, We are pleased to announce the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). Dates: April 6 - 16, 2015 Invited speakers: Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Victor Lamzin, Hamburg, Germany Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Rob Nicholls, Cambridge, UK Randy Read, Cambridge, UK William Shepard, Paris, France Pavol Skubak, Leiden, the Netherlands Clemens Vonrhein, Cambridge, UK A preliminary program, as well as the application forms and contact information, can be found in this www site <http://www.pasteur.edu.uy/index.php/es/futuroscursos>. (within the page, look for this workshop’s details) The www site will be updated regularly, so stay tuned. This activity is supported by the Reseau International des Instituts Pasteur (RIIP); the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Applicants: 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). The application deadline is February 16, 2015. The results will be announced by March 6. Please address further inquiries to: mx2015(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2 020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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neutron scattering table for specific metal isotope
by Maxime Cuypers 04 Dec '14

04 Dec '14

Hello, I would like to alter the neutron scattering table for phenix.refine so that it takes into account the correct bcoherent value for the metal isotope present in my structure. the difference is significative between the natural occurence bcoh... i have been looking around in chem_data but could not find the neutron scattering tables. does anyone have any idea where to look please? cheerios -- Dr. Maxime Cuypers

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adding hydrogens to custom peptide bonds
by Dale Kreitler 04 Dec '14

04 Dec '14

Hi All, I am trying to add riding hydrogens to a model that includes beta-3-homoglutamine (B3Q). The monomer is not in the ccp4 library but it is a PDB chemical component. So far I have used elbow to build and optimize my own version of the ligand using the atom naming convention for a beta-amino acid in the PDB (where CB is in the backbone adjacent to the amino group, so the backbone goes like C-CA-CB-N). I am using a TRANS cif link from the monomer library for the N(alpha-amino acid) to C(beta-amino acid), and I have defined my own cif link for the N(beta-amino acid) to C(alpha-amino acid). However when I run phenix.reduce I can't get hydrogens to appear on the peptide bonds between the beta-amino acid and adjacent alpha-amino acids (hydrogens appear every where else on the ligand and in the model). I realize the effect of two hydrogens on the model is inconsequential but I would like to figure out how I can get phenix.reduce to recognize the bonds to my "ligand" as standard peptide bonds and add hydrogens accordingly. Thanks, Dale -- Dale Kreitler Gellman Lab UW Madison, Department of Chemistry

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restraints between molecules in adjacent asymmetric units.
by jens j birktoft 04 Dec '14

04 Dec '14

Hi Everybody. Are there ways to restrain non-covalent interactions between molecules in adjacent asymmetric units? I know the custom bond procedure works well for covalent bonds. However I also would like to add restraints for (1) bond angles, (2) torsion angles (less important) and (3) nucleotide base-pairing. I know that all of these can be generated via the custom bond syntax, but that is a rather tedious and time-consuming process. Perhaps there is a simpler way I know this issue has been raised before but am unaware of any new developments. Cheers Jens -- +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Director of Crystallography Structural DNA Nanotechnology Chemistry Department, New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

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