- phenixbb - phenix-online.org

Mac backwards compatability
by Katherine Sippel 19 Dec '14

19 Dec '14

Hi all, I was trying to be a good child and update to the latest nightly build, but I noticed that the Mac options for dev-1893 and -1894 are all listed as OS X 10.9 rather than OS X 10.6.7+. I attempted to use the OS X 10.9 installer just to see if it would work (it does not). Is phenix no longer supporting older Mac OSs? I know you have more than enough OSs to keep track of, so there is no judgement in that statement. I am just trying to figure out if I am going to have to cave and begrudgingly update my OS. Thanks, Katherine -- "Nil illegitimo carborundum"* - *Didactylos

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secondary restraint refinement
by CPMAS Chen 17 Dec '14

17 Dec '14

Dear Phenix Users, How do I force some residues in a non-helix conformation? I have a 3A data, and have the protein model refined. But in some region, 3~4 residues are in the helix conformation, and the density fit is good. Anyway, let me say this, I want to force these residues in a non-helix conformation. I tweaked the model a little bit and load them in VMD, and make sure they are not helix anymore. I turn on secondary-structure-restraint in phenix, take out the helix remarks for these residues in the def file. but once the refinement is done, they are still in a helix region (phenix automatically secondary structure analysis, or viewed in VMD). Is there a feasible way to keep them away from helix conformation? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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number of alternate conformations allowed
by Scott Horowitz 17 Dec '14

17 Dec '14

Hi all, Does anyone happen to know the upper limit on the number of alternate conformations that phenix.refine can handle at once for a residue? From playing around with it, it seems that phenix.refine recognizes both letters and numbers in that position, but not a pound sign, so that would suggest it could at least handle 36, so long as I don't crash my computer trying that many. Is this correct, from anyone's experience/knowledge? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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how to use phenix.angle command?
by 李翔 16 Dec '14

16 Dec '14

Hi, I am trying to measure the angle between two DNA duplex domains. I used phenix.angle command for calculation. However, I get a wrong answer. Can anyone talk a little bit more details on this command please? I used a single strand DNA from each duplex to calculate the angle which I thought it might be working since it is calculating the axis. Thanks for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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Reliable twinning fraction estimation
by Xiao Lei 10 Dec '14

10 Dec '14

Dear All, I have a x-ray dataset of a protein-DNA complex to 2.8 A resolution with space group P312 checked by phenix xtriage for twinning. The estimated twin fraction from the output of xtriage is: 0.115 (Britton analysis); 0.119 (H test) and 0.022 (maximum likelihood method). However, the L-test graph in xtriage shows my observed data almost perfectly overlay with theoretical perfect twin data. In addition, when I tried to use phenix to do refinement with twin law -h,-k,l, the log file shows my twin fraction estimation is 0.49, which is very high and much bigger than Britton analysis and H test estimation. As far as my understanding is that if a twin fraction is lower than 15%, I still have hope to solve the structure (molecular replacement in this case) with reasonable R value, but if the twin fraction is 0.49, which is almost a perfect twin, which makes detwin impossible and refinement will stall at high R values (in my case, R free start: 0.4199; R work start: 0.4121; and R free final: 0.4038 and R work final: 0.3640 after running phenix refinement with twin law -h, -k, l). My question: which twin fraction estimation is more reliable? is my data almost perfectly twined? I attached the graphs of L test, Britton analysis and twin estimation from phenix xtriage and part of log file from phenix refine here. Many thanks in advance. Xiao

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Autobuild with "build semet residues"
by Todd Jason Green 10 Dec '14

10 Dec '14

Hello all- I have been trying to use autobuild with a semet dataset. I have checked the "build semet residues" option in the autobuild gui. At some point after the composite build, the error below is generated and the final model has been stripped of all semethionines. I am using phenix version 1.8.4-1496 on a macbook. I have now downloaded the new version. But can someone expand on my problem. My input sequence and model pdb contain Methionine but I expected the rebuild process to alter them. Should I change the one letter code for semet from m to something else. -Todd . . . . Final composite model # 1 : AutoBuild_run_11_/MULTIPLE_MODELS/model.pdb_1 Final composite mtz # 1 : AutoBuild_run_11_/MULTIPLE_MODELS/resolve_composite_map.mtz_1 AutoBuild_combine_iter AutoBuild Run 11 Wed Dec 10 14:51:18 2014 AutoBuild_combine AutoBuild Run 11 Wed Dec 10 14:51:18 2014 Done with combine finished AutoBuild Run 11 Wed Dec 10 14:51:18 2014 Finishing AutoBuild Run 11 Facts written to AutoBuild_run_11_/AutoBuild_Facts.dat Warnings: Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: NOTE: The following residues (and similar residues) from AutoBuild_run_5_/overall_ortho_best_bchain_molrep1_refmac1_semettomet_ed.pdb are not PROTEIN or do not match the sequence and will not be part of the building process : MSE B33, MSE B45, MSE B59, MSE B63, MSE B68, MSE B194, MSE B201, MSE B210, MSE B216, MSE B256, MSE B266, MSE B308, MSE A33, MSE A45, MSE A59, MSE A63, MSE A68, MSE A194, MSE A201, MSE A210, MSE A216, MSE A256, MSE A266, MSE A308, MSE C33, MSE C45, MSE C59, MSE C63, MSE C68, MSE C194, MSE C201, MSE C210, MSE C216, MSE C256, MSE C266, MSE C308, MSE D33, MSE D45, MSE D59, MSE D63, MSE D68, MSE D194, MSE D201, MSE D210, MSE D216, MSE D256, MSE D266, MSE D308, Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: Warning: some residues not rebuilt successfully on cycle 2: Chain 'A': 32, 44, 200, 217- 221, 280- 299, 314- 323, Chain 'C': 22- 32, 39- 44, 148- 152, 163- 167, 188- 193, 211- 215, 217- 221, 334- 336, Chain 'B': 32, 44, 118- 122, 193, 227- 231, 309- 318, Chain 'D': 12- 32, 34- 44, 46- 50, 143- 147, 158- 162, 188- 193, 334- 336 Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: Warning: some residues not rebuilt successfully on cycle 3: Chain 'A': 32, 39- 44, 193, 217- 226, 280- 294, Chain 'C': 22- 32, 34- 44, 46- 55, 153- 162, 193, 200, 211- 215, 217- 221, 242- 246, 324- 336, Chain 'B': 32, 44, 118- 122, 193, 262- 265, 319- 323, Chain 'D': 17- 32, 34- 44, 46- 50, 143- 162, 188- 193, 200, 334- 336

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Rigid body refinement at low resolution
by Jianghai Zhu 09 Dec '14

09 Dec '14

Hi all, I recently solved a complex structure at 8 Å. There are 3 molecules per asymmetric unit and each complex contains 8 domains. I was trying to do rigid body refinement in phenix.refine. However, all the rigid body refinement gave me worse Rfree, even at ultra-low resolution, and phenix.refine reversed the result to the original model. Anyway to make this rigid body refinement more stable? Is there a dampen factor in phenix.refine so that the program only moves a domain at a fraction of what it wants to, e.g. 1/2, 1/3… ? Thanks. Best, —Jianghai

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Not Updating Waters
by Ryan Henry Gumpper 09 Dec '14

09 Dec '14

Hi all, I am having an issue during refinement when using Phenix Refine. Every time I try to "update waters" it does not place or update the waters. My structure is 2.72 A. Is the resolution not good enough for this feature? If anyone has ideas, or if I need to supply more information, I would be happy to oblige as I am fairly new to the field and still learning. Thank you in advance!

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Ramachandran maps
by PC 09 Dec '14

09 Dec '14

Hi guys, Sorry for the repost in COOT/CCP4/PHENIX. It is possible on of the users in one of these communities might know the answer I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which I can superimpose my coordinates phi and psi? Something like what appears in COOT->Validate->Ramachandran Plot. How does one generate such images for publications? Thank you, Patrick ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth

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Challenging Mol.Rep. Problem
by Mo Wong 09 Dec '14

09 Dec '14

Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are round 9to12-ish copies in the ASU. The overall Rmerge is high at ~25% with I/sig cutoff ~2 and redundancy of 5; however, at 4.5A this drops to ~15%. Furthermore, processing in P1 gives similar Rmerge values too. Self-Patterson doesn’t suggest translational symmetry, but the self-rotation function (SRF) suggests high NCS (see below/attached). I’m hoping the SRF might be helpful in trying to confirm/dismiss C2 is the likely space group, and perhaps suggest a logical assembly with the ASU (I see strong 2-fold and 3-fold NCS operators suggesting to me dimeric trimers or vice versa - however, I’ve never had to really analyze SRFs in the absence of a mol. rep. solution so my interpretation could be wrong). Anyway, any help to bringing a molecular replacement solution closer to reality would be appreciated. Thanks! [image: Inline image 1]

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Re: [phenixbb] [ccp4bb] MR_ROSETTA
by Terwilliger, Thomas Charles 09 Dec '14

09 Dec '14

Hi Bashir, It is probably something very small to fix...can you send me the result of doing this: echo $PHENIX_ROSETTA_PATH echo $ROSETTA3_DB/ ls $PHENIX_ROSETTA_PATH//main/source/bin/mr_protocol* On my machine I get: [terwills-MacBook-Air:~] terwill% echo $PHENIX_ROSETTA_PATH /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle [terwills-MacBook-Air:~] terwill% echo $ROSETTA3_DB/ /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle/main/database/ [terwills-MacBook-Air:~] terwill% ls $PHENIX_ROSETTA_PATH//main/source/bin/mr_protocol* /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle//main/source/bin/mr_protocols.macosclangrelease /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle//main/source/bin/mr_protocols.python.macosclangrelease All the best, Tom T Could some body explain why I am getting the error message when running MR-Rosetta. Message is " Sorry cannot locate a binary starting with mr_protocol.default' in the directory /home/phenix/rosetta_2014.34.57213_bundle/main/source/bin I just download it and locate it in the preferences, wizard and then path to Rosetta. Thanks Bashir -- Muhammad Bashir Khan ************************************************** Department of Biochemistry University of Alberta, Canada Canada

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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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Intl Conf on Structural Genomics 2015: "Deep Sequencing Meets Structural Biology"
by Terwilliger, Thomas Charles 04 Dec '14

04 Dec '14

Dear Colleagues, We hope that you will be able to attend 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. 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. 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] · PHENIX: Automated determination of molecular structures · HKL3000: From X-ray diffraction images to structure determination in minutes · Approaches to the translation of deep sequencing data into three-dimensions · Protein expression and characterization workshop · Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure & Function You can see all the details of the conference at http://www.weizmann.ac.il/conferences/ICSG2015 . 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! Invited Speakers will include: Keynote Speakers: Shamil Sunyaev - Harvard Medical School Janet Thornton – EMBL/EBI - The FEBS National Lecturer Speakers: Arie Admon – Technion, Haifa Lucia Banci - CERM, University of Florence Pamela J. Bjorkman – CalTech, Pasadena Samir K. Brahmachari - CSIR-Institute of Genomics & Integrative Biology, Delhi Susan Buchanan - NIDDK, NIH, Bethesda Mark Gerstein - Yale University, New Haven Wayne Hendrickson - Columbia University Medical Center, New York Yvonne Jones - University of Oxford Luhua Lai - Peking University, Beijing Michael Levitt – Stanford University Michal Linial – The Hebrew University of Jerusalem Abraham Minsky - Weizmann Institute of Science, Rehovot John Moult - IBBR, University of Maryland, Rockville Nathan Nelson - Tel Aviv University Stefan Raunser - MPI of Molecular Physiology, Dortmund Monica Roth - Rutgers University, Piscataway Dinakar M. Salunke – Regional Centre for Biotechnology, Gurgaon Eran Segal - Weizmann Institute of Science Philip Selenko - Leibniz Institute of Molecular Pharmacology (FMP Berlin) Sachdev Sidhu - University of Toronto Rotem Sorek - Weizmann Institute of Science Jan Steyaert - VIB, Flanders, Brussels Dan Tawfik - Weizmann Institute of Science Gunnar von Heijne - Stockholm University Soichi Wakatsuki - Stanford University Shigeyuki Yokoyama - Genomic Sciences Center, RIKEN Yokohama Institute Ada Yonath - Weizmann Institute of Science Mingjie Zhang – Hong Kong University of Science & Technology 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 Organizing 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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Phenix.ensemble_refinment questions
by Joseph Brock 04 Dec '14

04 Dec '14

Dear Phenix community, I was hoping that some of you may be able to clarify some questions about Phenix.ensemble_refinement: 1. In the associated publication (Burnley et al. eLife 2012;), the ensemble refinement is validated by comparing the correlation of the ensemble generated map, with the map generated from the experimental phases for PDB entry 1YTT ("The overall correlation coefficient between the electron-density map from the ensemble model (obtained without experimental phases) and the experimentally phased electron-density map was 0.903, compared with 0.873 and 0.895 for the published and re-refined single structures. These seemingly small improvements in over- all quality indicators allow for significant local improvements."). I am confused how one computes an experimentally phased from structure factors deposited in the PDB that contain only anomalous intensities/amplitudes and not Hendrickson-Lattman coefficients. Is there a program within the phenix package that can do this? In addition, the phenix.ensemble_refinement keywords include: * experimental_phases * file_name = None * labels = None * Is it possible to include experimental phases during the rolling average refinement process and could this be beneficial (if the phases were of a sufficient quality)? 2. Is the correct procedure in parameter optimisation to optimise pTLS, then temperature offest and then tx? Or is it possible that the best ensemble may be generated from any (non-directional) combination of the above parameters? 3. What is the function of the "nproc" keyword? If this is the number of CPU cores that can be used in parallel, what is the most efficient way of using phenix.ensemble_refinement on a cluster? 4. Can anybody suggest a good way to compare the ensembles generated by phenix.ensemble_refinement with the trajectories of traditional MD simulations (for e.g. produced by NAMD? ;) Finally, I noticed that I cannot run phenix.ensemble_refinement using a "my_parameters.eff" file, it is necessary to type on the command line. Alternatively, the queueing system for the supercomputer I use is managed by SLURM, however, I cannot submit batch jobs via the appropriate command sbatch with anything other than default parameters (keywords in a parameters.eff or that are typed explicitly following the mycoords.pdb mydata.mtz myrestraints.cif files are not incorporated into the resulting parameters of the .log file). Could these issues be due to my local environment setup? I am running Phenix 1.9-1692 Platform: intel-linux-2.6-x86_64 redhat-e6.5. Sorry for the long email and many thanks in advance for you help! Best regards, Joseph. Joseph Brock | PhD Division of Physiological Chemistry II Department of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 SE-171 77 Stockholm, Sweden

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Fwd: PostDoc position at the ALS
by Peter Zwart 03 Dec '14

03 Dec '14

Dear Colleagues, The Advanced Light Source in Berkeley is now looking to recruit two Postdocs to develop scattering in the tender X-ray regime. In particular using the Phosphors and Sulfur k-edge to enhance scattering. Details may be found here: *http://jobs.lbl.gov <http://jobs.lbl.gov/> * Postdoctoral Researcher - TReXS (Materials/ Physical Science)-80316 *and* Postdoctoral Researcher - TReXS (Biophysical Sciences)-80317 Alexander Hexemer and Peter Zwart Lawrence Berkeley National Lab -- ----------------------------------------------------------------- P.H. Zwart Staff Scientist Berkeley Center for Structural Biology, Science lead Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 SASTBX: http://sastbx.als.lbl.gov BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org -----------------------------------------------------------------

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pdb file error
by maher alayyoubi 03 Dec '14

03 Dec '14

Hi Everyone, I am having a problem of phenix.refine not accepting a pdb file that I just finished editing in coot. It is a protein RNA compplex where the protein part was built in buccaneer and the RNA strand built in nautilus. I assembled the final model by text editing the pdb file and adding the RNA part. Whenever I feed this pdb file into phenix, it comes back with two errors: " number of atoms with unknown unbonded energy type symbols:6" . "The coot command could not be located" Does anyone know how to fix this problem? I tried converting the file into mmcif and feeding it to phenix but the same error comes back again. Thank you very much, Maher

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