- 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

2 1

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 ******************************************************

2 1

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

2 1

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

2 1

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

3 6

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

2 1

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

3 2

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!

2 1

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

2 1

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]

1 0

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

1 0

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.

2 3

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

2 1

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

3 9

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.

1 0

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

1 0

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

3 4

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

1 0

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

6 13

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

2 1

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 +++++++++++++++++++++++++++++++++++++++++++++++++++

3 2

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 = = = = = =

1 0

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

6 9

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 -----------------------------------------------------------------

1 0

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

2 1

norleucine (NLE) restraints
by Daniel Keedy 01 Dec '14

01 Dec '14

Hi everybody, First-time poster! I'm trying to re-refine 2f4k.pdb, but phenix.refine chokes on the non-standard norleucine (NLE) amino acid. I've tried phenix.elbow and phenix.ready_set using different version of PHENIX, with the NLE cards as either HETATM or ATOM, all to no avail. SHELX was used to refine the structure originally, but I'd like to use PHENIX to re-refine it. Any ideas on how to define these restraints? Daniel Keedy James Fraser Lab UCSF

3 3

来自"张士军" <[email protected]>的邮件
by 张士军 01 Dec '14

01 Dec '14

hello everyone how could use phenix phasing to phase a se substructure by search any possible spacegroup

1 0

Generate table 1-error message
by Lau Sze Yi (SIgN) 30 Nov '14

30 Nov '14

Hi, I got an error message when I tried to run the generate table 1 utility: Crystal symmetry mismatch between different files. My input files for pdb, mtz and cif were generated from my ccp4 refmac run. The unmerged data is the mtz output of ccp4 aimless. Did I upload the wrong file? Regards, Sze Yi Research Fellow Singapore Immunology Network (SigN) 8A Biomedical Grove, #03-06 Immunos, Singapore 138648 DID: +65 6407 0640 Fax: +65 6407 0640

2 1

Not a suitable array of R-free flags:
by Yamei Yu 26 Nov '14

26 Nov '14

Dear all, I use phenix.refine to refine a structure. Firstly, I used --dryrun to generate an .eff file. The command is "phenix.refine --dry_run 7_44.mtz 7_44.pdb refinement.input.xray_data.r_free_flags.generate=True refinement.input.xray_data.r_free_flags.max_free=1000” Then I use run the program by typing “phenix.refine 7_44_refine_001.eff” It runs correct! After that I use coot to modulate some parts of the structure, then I want to refine the structure again. I type “ phenix.refine 7_44_refine_002.def” This time I got the following error message: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked the generated file by phenix “7_44_refine_data.mtz” I does contain a column labeled as R-free-flags. I paste part if it below. * Space group = 'P1' (number 1) OVERALL FILE STATISTICS for resolution range 0.000 - 0.277 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC -32 31 0 100.00 -2.2 11.9 49.44 1.90 H H 2 NONE -46 45 0 100.00 -2.5 17.8 49.44 1.90 H K 3 NONE 0 49 0 100.00 18.8 18.8 49.44 1.90 H L 4 NONE 0.9 271.3 0 100.00 26.52 26.52 49.44 1.90 F F-obs 5 NONE 0.2 5.1 0 100.00 1.25 1.25 49.44 1.90 Q SIGF-obs 6 NONE 0.0 1.0 0 100.00 0.01 0.01 49.44 1.90 I R-free-flags No. of reflections used in FILE STATISTICS 143215 Then I regenerate a new mtz file with FreeRflag by XDSCONT, then I revise the .def file accordingly and rerun the program. I got same error message:Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked my new mtz file, it dose contain a column labeled as FreeRflag Why there is an error message? How to solve it? Thank you so much!! Best wishes! yamei ************************************************ Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyuxtal(a)gmail.com ymyuxtal(a)163.com yamei_yu(a)scu.edu.cn

3 2

error messages running phenix.mr_rosetta
by Ursula Schulze-Gahmen 26 Nov '14

26 Nov '14

I am running mr_rosetta on a 64bit Linux computer. The model optimization worked without a problem, but now in the molecular replacement step I am receiving error messages, and I am not sure what the problem is. Could anyone provide a suggestion? Thanks Ursula /usr/share/themes/Slider/gtk-2.0/gtkrc:80: error: unexpected identifier `colorize_scrollbar', expected character `}' Fontconfig warning: no <cachedir> elements found. Check configuration. Fontconfig warning: adding <cachedir>/var/cache/fontconfig</cachedir> Fontconfig warning: adding <cachedir>~/.fontconfig</cachedir> (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Pango-WARNING **: Failed to load Pango module '/programs/x86_64-linux/phenix/dev-1819/phenix-dev-1819/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so' for id 'BasicScriptEngineFc' (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Gtk-WARNING **: Could not find the icon 'system-file-manager'. The 'hicolor' theme was not found either, perhaps you need to install it. You can get a copy from: http://icon-theme.freedesktop.org/releases -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

1 0

residue selection for rsrl?
by Kevin Jude 26 Nov '14

26 Nov '14

I am refining a structure at 2.9 Å resolution and have two side chains that keep moving out of density during reciprocal space refinement; both side chains should fit the resulting Fo-Fc density in favored rotamers. Turning on real-space refinement fixes this problem but leads to higher Rfree and poorer geometry overall. Can I select a subset of residues for real space refinement while still performing reciprocal space refinement on the whole asymmetric unit? Thanks for any help Kevin

2 2

phenix rosetta refine
by Andreas Förster 26 Nov '14

26 Nov '14

Dear all, I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit. However phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log& fails with the following error in log: End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. To me it seems things are defined correctly: andreas@csbstereo in phenix: echo $ROSETTA_BIN /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin andreas@csbstereo in phenix: ls $ROSETTA_BIN | grep scripts rosetta_scripts.linuxgccrelease@ rosetta_scripts.default.linuxgccrelease@ andreas@csbstereo in phenix: ll $ROSETTA_BIN/rosetta_scripts.linuxgccrelease lrwxrwxrwx 1 csbadmin csb 93 Oct 9 2013 /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -> ../build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease Any idea of what's wrong would be greatly appreciated. Andreas -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London

3 2

Alternative conformation of ligand with near zero occupancy
by Singh, Bishal 26 Nov '14

26 Nov '14

Hello everybody, I thank you for clarifying my previous doubts. Your suggestions matter a lot to me. Here I have another doubt. I have structure of a protein in complex with triglycan (fucose-galactose-galactose). The terminal galactose of this triglycan possesses two conformations with occupancies 0.4 and 0.6. In order to satisfy the geometric parameters of this triglycan, I derived the alternative conformation of fucose and the central galactose as well. Then I performed occupancy refinement. The occupancy of alternative central galactose is 0.06 and that of alternative fucose is 0.00. Now the question is, should I delete this fucose of zero occupancy or keep it to maintain the geometric parameters of triglycan? I am looking forward for your opinion. If you like I can provide a snapshot of ligand with electron density. With regards, Bishal Singh PhD student DKFZ, University of Heidelberg, Germany

2 1

input for specifying labin in phenix.find_ncs
by Arka Chakraborty 26 Nov '14

26 Nov '14

Dear Phenix BBers, I have a seemingly trivial problem in specifying column labels in phenix.find_ncs. Following the manual, on entering labels as : phenix.find_ncs xx.pdb yy.mtz params.ncs.labin = "labin FP=F PHIB=PHI FOM=FOM" , phenix returns the error : 'Sorry, cannot interpret the keyword: params.ncs.labin=labin FP=F PHIB=PHI FOM=FOM'. Any clues on what mistake I might be making will be greatly appreciated. Thanks a lot, Regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

3 4

Different space group of coordinate and structure factors
by Singh, Bishal 25 Nov '14

25 Nov '14

Hello everybody, For a data-set, the space group after data-processing was P4222. When I performed molecular replacement through PHASER in phenix keeping the search option 'All possible in same point group", the space group changed to P41212. Now the question is that shall I process the data again in this new space group or should I move on for refinement? Please suggest me your opinion. With regards, Bishal Singh PhD Student DKFZ, University of Heidelberg, Germany

2 2

explicit solvent in low resolution refinement
by Guenter Fritz 25 Nov '14

25 Nov '14

Dear all, we have determined the structure of a protein complex at 3.5 A resolution as well as the structures of three subunits of this complex independently at resolutions better than 2 A. I had used the models of the subunits as reference models in refinement, perfect. Now I was wondering whether one could use explicit solvent positions (e.g. inner shell water molecules) from the high resolution structures in the low resolution refinement. This should be superior to a simple bulk solvent model. I placed the inner shell water molecules from the high res structures into the low res model and added harmonic restraints to the water positions in low res refinement. I see a decrease of about 0.5% in Rwork and Rfree versus the model without water molecules. However, adding harmonic restraints excludes the option to use the reference models in refinement. Is it possible to use protein and water atoms from the reference models to generate restraints for the low resolution refinement? Thank you, Guenter

5 9

ready set and H/D addition on waters
by Maxime Cuypers 24 Nov '14

24 Nov '14

hello, after not using phenix for a while, i just realised the new versions do not include the option in ready_set gui to add H or D atoms to waters in the pdb models (and only to the waters without altering the rest of the model would be nice). of course it can be done on the command line but why has it been removed? it is a very neutron crystallographer friendly option don t you think? cheerios, -- Dr. Maxime Cuypers

3 4

Rwork > Rfree
by Singh, Bishal 21 Nov '14

21 Nov '14

Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany

4 3

MRage against local "select" PDB database on commandline
by Kaushik Hatti 21 Nov '14

21 Nov '14

Hi, I am new to Phenix. Sorry if my question is naive. For a given mtz file, I want to pick templates from a local PDB database (its actually iTasser template library) and perform Molecular Replacement using MRage. I have already installed Blast, downloaded iTasser PDB library (http://zhanglab.ccmb.med.umich.edu/library/PDB.tar.bz2) and extracted sequences from both the downloaded PDB template library set and target protein for which mtz is available. How should I go about building pipeline to perform MR using templates from locally downloaded select PDB database? Are there any more parameters available for parameter name: services under scop: search other than "local" and "ncbi"? Thanks in advance, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

2 6

Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 20 Nov '14

20 Nov '14

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2015 issue is 17 December 2014 (with some leeway if you are still working on the text, especially as it can be polished over the break). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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

1 0

Re: [phenixbb] Rwork > Rfree
by Ed Pozharski 20 Nov '14

20 Nov '14

Generate a different test set and repeat refinement. Do it twenty times. If R turns out to be systematically higher than Rfree even in few resolution shells, you have an interesting case worth looking at. If not, it's just noise. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: "Singh, Bishal" <b.singh(a)dkfz-heidelberg.de> </div><div>Date:11/20/2014 9:52 AM (GMT-05:00) </div><div>To: phenixbb(a)phenix-online.org </div><div>Subject: [phenixbb] Rwork > Rfree </div><div> </div>Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

1 0

GeoStd: was definition of glycosylation in phenix.refine
by Schubert, Carsten [JRDUS] 18 Nov '14

18 Nov '14

Hi Nigel, could you please comment on any plans to harmonize the use of these restraints for other refinement programs as well. Phenix originally appears to have implemented the restraint dictionaries from CCP4. Right now there seems to be some kind of parallel development going on with the dictionaries being in sync to some degree. Is there a plan to move to a unified restraints distribution at some point? Thanks Carsten From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Nigel Moriarty Sent: Tuesday, November 18, 2014 12:38 PM Cc: PHENIX user mailing list Subject: Re: [phenixbb] definition of glycosylation in phenix.refine @Laurent Engin advice is sound but you are having trouble free feel to send me the inputs directly. NB. Any files sent to me will be held in strictest confidence. @Engin I think you will find what you are looking for in the GeoStd. As restraints are improved, they are moved from $PHENIX/chem_data/mon_lib to $PHENIX/chem_data/geostd (which is hosted on SourceForge for anybody's use). The directory structure is the same as the Monomer Library with a geostd_list.cif file corresponding to mon_lib_list.cif which specifies the links. 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<mailto:[email protected]> Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> On Tue, Nov 18, 2014 at 8:25 AM, Engin Özkan <eozkan(a)uchicago.edu<mailto:[email protected]>> wrote: Hi Laurent, If I am reading the error message right, you did not delete the hydrogens that get removed upon bond formation. That's what it is complaining about. I always thought Phenix probably removed these atoms (the hydroxyl and the hydrogen) automatically when you defined the link, but never tested if it really does it. I also usually remove all hydrogens right away when sugar residues are inserted. Finally, I will recommend that you use automatic linking in the phenix.refine GUI. It works great (I am on the latest nightly, dev-1839; you may need to upgrade). No need to define pesky links anymore. Thank you developers! At the risk of hijacking the thread, I could not find in my installation the cif files for N-linked sugars. Have they been moved elsewhere? Hope this helps, Engin On 11/18/14 10:02 AM, Laurent Maveyraud wrote: Hi, I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links... The glycosylatin is Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064 This is what I add in the eff file : apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain D and resname NAG and resid 1061 residue_selection_2 = chain A and resname ASN and resid 638 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname NAG and resid 1062 residue_selection_2 = chain D and resname NAG and resid 1061 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname BMA and resid 1063 residue_selection_2 = chain D and resname NAG and resid 1062 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain D and resname MAN and resid 1064 residue_selection_2 = chain D and resname BMA and resid 1063 } this is correctly read in refine: apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain D and resname NAG and resid 1061 residue_selection_2: chain A and resname ASN and resid 638 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname NAG and resid 1062 residue_selection_2: chain D and resname NAG and resid 1061 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname BMA and resid 1063 residue_selection_2: chain D and resname NAG and resid 1062 apply_cif_link: data_link: ALPHA1-3 mod_id_1: DEL-HO3 mod_id_2: DEL-O1 residue_selection_1: chain D and resname MAN and resid 1064 residue_selection_2: chain D and resname BMA and resid 1063 but generates an error : Number of atoms with unknown nonbonded energy type symbols: 5 "HETATM10951 HO4 NAG D1052 .*. H " "HETATM10973 HO4 BMA D1053 .*. H " "HETATM11028 HO4 NAG D1062 .*. H " "HETATM11050 HO4 BMA D1063 .*. H " "HETATM11070 HO3 MAN D1064 .*. H " and the job stops. Any ideas on what if wrong ? thanks for your help Laurent _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

1 0

definition of glycosylation in phenix.refine
by Laurent Maveyraud 18 Nov '14

18 Nov '14

Hi, I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links... The glycosylatin is Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064 This is what I add in the eff file : apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain D and resname NAG and resid 1061 residue_selection_2 = chain A and resname ASN and resid 638 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname NAG and resid 1062 residue_selection_2 = chain D and resname NAG and resid 1061 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname BMA and resid 1063 residue_selection_2 = chain D and resname NAG and resid 1062 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain D and resname MAN and resid 1064 residue_selection_2 = chain D and resname BMA and resid 1063 } this is correctly read in refine: apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain D and resname NAG and resid 1061 residue_selection_2: chain A and resname ASN and resid 638 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname NAG and resid 1062 residue_selection_2: chain D and resname NAG and resid 1061 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname BMA and resid 1063 residue_selection_2: chain D and resname NAG and resid 1062 apply_cif_link: data_link: ALPHA1-3 mod_id_1: DEL-HO3 mod_id_2: DEL-O1 residue_selection_1: chain D and resname MAN and resid 1064 residue_selection_2: chain D and resname BMA and resid 1063 but generates an error : Number of atoms with unknown nonbonded energy type symbols: 5 "HETATM10951 HO4 NAG D1052 .*. H " "HETATM10973 HO4 BMA D1053 .*. H " "HETATM11028 HO4 NAG D1062 .*. H " "HETATM11050 HO4 BMA D1063 .*. H " "HETATM11070 HO3 MAN D1064 .*. H " and the job stops. Any ideas on what if wrong ? thanks for your help Laurent -- ---------------------------------------------------------- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département Biologie Structurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 ----------------------------------------------------------

3 3

mrage with nucleic acids?
by Paul Paukstelis 17 Nov '14

17 Nov '14

I'm trying to run mrage with nucleic acid models. With phaser, it is possible to specify the molecule type, but this option doesn't exist in mrage (from what I can see). Providing a sequence file automatically assumes protein one letter codes. Any suggestion on how to clearly define a sequence file as a nucleic acid? Thanks, --paul

2 1

Filtering CCP4 maps to lower resolution
by Barad, Ben 16 Nov '14

16 Nov '14

Hi All, I am currently trying to filter a CCP4-formatted real space map from the EMDB, which is at 3.2 Å resolution, to different resolutions from 3.2 to 5 Å, and I've been having a bit of a difficult time getting it to work. My first thought was to do an fft to get structure factors, then regenerate the map from those structure factors with a resolution cutoff. To do this, I used the tools "phenix.map_to_structure_factors" and "phenix.mtz2map" to generate a structure factor file, then convert it back into a map. When I do this, I end up with a very noisy map that is not usable for what I would like to do. Is there a better way to accomplish this in phenix (or another tool)? I've also tried some low-pass filtering with proc3d, without much success... Thanks, Ben Barad Fraser Lab @ UCSF

3 3

Re: [phenixbb] simulated annealing omit map
by Pavel Afonine 15 Nov '14

15 Nov '14

Hello Bishal, as discussed before, computing ligand-omit map is tricky. Quoting my previous email: """ There are two commonly used options for omitting the ligand in order to demonstrate its presence/absence in Fo-Fc OMIT map: 1) Physically remove the ligand from PDB file. Then do some refinement and calculate Fo-Fc map. 2) Keep ligand in the file, set its occupancy to zero. Then, again, do some refinement and calculate Fo-Fc map. In this case you may want to ask refinement program to not move the ligand or move it only a little. Now, here is why these two options are poor and will not give you what you want. In the first case the bulk-solvent mask will be set in the ligand region and therefore it will mask ligand density (bulk-solvent will be filled into the ligand region). Depending on the strength of ligand density it may be masked completely or deteriorated. If you follow the second option you will always get positive density in ligand area. This density may correspond to bulk-solvent, ligand or mixture of both. That is there will be no simple way to differentiate whether this density arises from the ligand or bulk-solvent. """ Dale Tronrud offered a great alternative option: """ An alternative you might want to consider is what I call the "discovery map". At some point in the refinement process there was a map that convinced YOU that this ligand was present. You should be the hardest person to be convinced so that map will be both an omit map (because the model had been refined without the ligand prior to this) and clear enough to satisfy the reader. """ Now, recently I improved composite OMIT map calculation in phenix.composite_omit_map tool, see picture that illustrates how it works: https://www.dropbox.com/s/dbp8e0348v5p78h/fig_6.png?dl=0 I think at present that's the best option to follow if for some reason you cannot follow Dale's suggestion. Pavel On 11/13/14 6:58 AM, Singh, Bishal wrote: > Hello everybody, > I am generating figures showing the electron density map around the > ligands. I deleted the ligands from final co-ordinate file and then > performed refinement with identical parameters as before while > keeping simulated annealing=true. I shall be thankful if someone could > suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. > Kindly also tell me the minimum acceptable contour level required for > showing difference map. All structures are at 1.4 - 2.0 angstrom > resolutions. > > Regards, > Bishal

5 5

CB outliers
by George Devaniranjan 13 Nov '14

13 Nov '14

Hi, I refined a structure using phenix.refine. The R/R free decreased slightly from 13.46/15.87 to 13.0/15.6. But, molprobity said there were 3 CB outliers (starting from 0). I looked at those residues in COOT. I could NOT really see a different between the refined and initial model. In addition I looked at COOT validate-->density fit analysis I cannot see ANY difference in the peak heights (same numerical value too). I looked at RSCC (using phenix validate tools as well). I still can't see a difference in the plots. I am not sure how to get rid of the 3 CB outliers that have crept in since I can't pick them out as worse off in the refined model. I ask since in another case > 3 CB outliers, with the same results in picking them out in COOT/RSCC. I am wondering if there is another way I can see the deviation and fix it? Thank you, George

3 6

Rosetta compile problem
by miyatake 13 Nov '14

13 Nov '14

Dear all, I tried to compile Rosetta for rosetta_refinement, on Mac OX10.10. I run " /rosetta_2014.22.56873_bundle/main/source] user% sudo scons.py But it was in failure, showing the following message: g++-4.2 -o build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os -c -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -m64 -march=nocona -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION=\"0\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -Ibuild/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/sqlite3 -Iexternal/dbio/sqlite3 -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include external/dbio/cppdb/atomic_counter.cpp sh: g++-4.2: command not found scons: *** [build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os] Error 127 scons: building terminated because of errors. How can I resolve that? Best regards, H. Miyatake

3 2

simulated annealing omit map
by Singh, Bishal 13 Nov '14

13 Nov '14

Hello everybody, I am generating figures showing the electron density map around the ligands. I deleted the ligands from final co-ordinate file and then performed refinement with identical parameters as before while keeping simulated annealing=true. I shall be thankful if someone could suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. Kindly also tell me the minimum acceptable contour level required for showing difference map. All structures are at 1.4 - 2.0 angstrom resolutions. Regards, Bishal

1 0

Settings-Directories of MR-Rosetta wizard is altered when phenix-GUI is restarted?
by Martin Moche 13 Nov '14

13 Nov '14

Dear colleagues, When restarting phenix followed by opening the "MR-Rosetta(beta)" the Settings-Directories need to be reset each time? How can I set Rosetta binary directory name: Rosetta binary name: Rosetta script directory name: Rosetta database directory name: in Settings-Directories of "MR-Rosetta(beta)" wizard (or elsewhere) so that they do not change each time I restart the phenix-GUI? These settings are not changed: Base output folder: Rosetta path: Likely "Rosetta path" does not change between phenix-GUI restarts since PHENIX_ROSETTA_PATH is set in the shell as: echo $PHENIX_ROSETTA_PATH /software/apps/rosetta/2014.35/gcc01/rosetta_2014.35.57232_bundle The "Path to Rosetta" in "Phenix preferences - Wizards" is currently left blank since $PHENIX_ROSETTA_PATH is set in the shell. I have by accident started a few jobs with mixed (new and old) settings and phenix-GUI starts without error messages and all processors are running 100% CPU, however likely in some infinite loop since no work is performed beyond "place model"... Best regards, Martin Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

1 0