- phenixbb - phenix-online.org

Phaser-EP log file
by Nishant Pandey 28 Feb '16

28 Feb '16

Hi,I have a confusion regarding solving iodine SAD-data in Phaser-EP.1. GUI result shows Log-likelihood gain: 115037.70 and FOM: 0.527. But in log file SAD Refinement Table (Sorted) ----------------------------- SET SpaceGroup FOM Log-Likelihood Rfac Composition I # 1 P 21 21 2 0.53 -115038 69.4 23 Why there is negative value of Log-Likelihood in log file? Is Log-Likelihood and Log-likelihood gain is two different things?Has Phaser solved it? When I feed these results to Autobuild, the model was ~80 % complete with Rfree and Rwork of 0.3171 and 0.2754 and Model Map correlation 0.74. Model was further refined in phenix.refine upto Rfree = 0.27. 2. When I am solving same dataset with Autosol and Autobuild, the dimer orientation have changed? Is this 'normal' or one of the solution is wrong and if it then which one should choose to refine further? Thanks in advance.

2 1

phenix.elbow with Gamess, no cif restraint file
by Dyda 26 Feb '16

26 Feb '16

Hi All, I'm clearly doing something wrong, but don't know what. Trying to run elbow with Gamess from the command line for "myligand" but no .cif file is produced. The input is a pdb file of the ligand, this the best I have. The command line: phenix.elbow --all-residues --do-all --gamess --basis=3D"3-21G" myligand.pdb > elbow.out & Everything seems to be OK, Gamess is found and run: > more elbow.out ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.10.1-2155 None - Nigel W. Moriarty (NWMoriarty(a)LBL.Gov) ------------------------------------------------------------------------------ Random number seed: 3628800 Initial processing time : 0.01 seconds 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P Input format is PDB MoleculeClass : C:15 O: 6 Cr: 1 (PDB format) 22 atoms 0 bonds 0 angles 0 dihedrals 0 rings 0 chirals Predicted memory usage by semi-empirical method : 41Mb Timing estimates Python portion / ATP : 62% c++ optimisation cycle / ATP : 47% Hydrogens may be required to determine the correct bonding Residue has metal at the centre of a coordination sphere. Using input geometry to generate restraints. Hydrogens may not be added. 0:10 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H 1:49 ReCentre molecule for optimisation ReCentre molecule for optimisation ReC Optimisation software : GAMESS Quantum method : UHF Quantum basis set : 3-21G Opt steps : 60 Opt macro steps : 3 Searching for flowchart file: flowchart.py searching: /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155/modules/elbow ****************************************************************************** filename : /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155/modules/elbow/flowchart.py FOUND ****************************************************************************** searching: /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155 searching: /home/dyda/.elbow searching: /home/dyda searching: /spin1/users/dyda/myligand Machine has 24018 Mb total memory 14687 Mb free memory Setting 1000 Mb max memory usage Searching for template run file: GAMESS.csh searching: /spin1/users/dyda/myligand ****************************************************************************** filename : /spin1/users/dyda/myligand/GAMESS.csh FOUND ****************************************************************************** Using /spin1/users/dyda/myligand/GAMESS.csh as input run file template all .inp, .dat, .gam files are produced, no errors, but no cif file. Thanks. Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

1 0

script to calculate phase error
by Kaushik Hatti 25 Feb '16

25 Feb '16

Hello, I understand Phase error is written out after phenix.refine. For a particular case, I need to calculate phase error during different stages of model building (before refinement). Is there a script available which could calculate phase error given a model(PDB) and structure factors (MTZ) files? Thanks, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

2 2

Separate cif files for the same nucleoside analog in it's monophosphate or triphosphate form?
by Zhe Li 25 Feb '16

25 Feb '16

Hi, I’m working on several protein/ligand structures, where the ligand is a novel nucleoside analog inhibitor. In each structure the ligand is either non-covalently bound as a ligand-5’-triphosphate (TP), or covalently bound to the protein as ligand-5’-monophosphate (MP). Do I need to create different cif file for ligand-MP and ligand-TP, or phenix can recognize the phosphates and there is no need for that? Thank you.

3 2

Multiple conformations
by Alejandro Virrueta 25 Feb '16

25 Feb '16

This is not exactly phenix specific, but I was wondering what are some commonly used methods to determine and validate the presence/occurrence of multiple conformations for a given amino acid? I am currently refining (for 5 cycles) a pdb with the occupancy of atoms of a specific residue set to 0, and then looking at the difference density map contoured to 3 sigma for extra density. Is this somewhat correct? What else could/should I do? Would using OMIT maps help? (What are OMIT maps, and how do I generate them?) Thanks, Alex (not a crystallographer)

4 4

How to include restrains to DNA as A-DNA or B-DNA
by Zhe Li 23 Feb '16

23 Feb '16

I am refining a protein-dsDNA complex structures at 2.4-3 A. Based on the phosphate distance, I can predict if particular nucleotide is A DNA (C3’-endo) or B DNA (C2’-endo). I want to add restrain to to the specific nucleotides as A or B DNA. But secondary_structure_restraints for nucleic acid does not seem to have options for this. Any suggestions? Thanks

3 2

Course on “Integrating X-ray crystallography and scattering with electron microscopy” - Oeiras (Portugal)
by Jose Artur Brito 23 Feb '16

23 Feb '16

Dear Colleagues, we hereby announce a 4-day course on “Integrating X-ray crystallography and scattering with electron microscopy”. The course is funded by i-NEXT and will be held at NOVA ITQB, Oeiras (nearby Lisbon), Portugal, May 2 to 5, 2016. The course covers a multidisciplinary approach to study the structure of challenging proteins, focusing on membrane proteins and large complexes. The basic principles will be provided for each addressed technique (Macromolecular Crystallography, Mass Spectrometry and Electron Microscopy); their applications in biological systems, major benefits and limitations will also be discussed. The Workshop is organized with lectures in the mornings followed by hands-on training. The course is aimed primarily at PhD students and young Post-Doctoral researchers interested in Structural Biology. Confirmed speakers are Jose Maria Carazo, Dmitri Svergun and Isabel de Moraes. Participants will be limited to 20. Candidate selection will be based on a short CV, a motivation letter from the applicant, and a recommendation letter from the supervisor. Registration deadline is February 23. Please send your application to combstruct2016(a)itqb.unl.pt. Registration fee is 180Eur including accommodation. More information can be found at http://www.itqb.unl.pt/combstruct2016 The Organizers, Margarida Archer, José A. Brito (ITQB-UNL) and Jose Maria Carazo (CNB-CSIC) -- ************************************************** * Jose Artur Brito, PhD * * Post-Doctoral Fellow * * Membrane Protein Crystallography Laboratory * * Instituto de Tecnologia Quimica Biologica * * Avenida da Republica, EAN * * 2780-157 Oeiras * * PORTUGAL * * * * Telephone - +351 214 469 761 * * Mobile - +351 962 452 179 * * Fax - +351 214 433 644 * * * * E-mail - jbrito(a)itqb.unl.pt * * Website - http://mx.itqb.unl.pt/ * **************************************************

1 1

CCP4 crystallographic summer school at the APS, June 21 - 29, 2016
by Sanishvili, Ruslan 23 Feb '16

23 Feb '16

Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

Rebuild fails in Rosetta-MR
by Rhys Grinter 22 Feb '16

22 Feb '16

Dear all, I'm currently trying to improve an model for a difficult MR problem using Rosetta-MR, When the program gets to the Rebuild stage it fails with the following message: *Error message:* child process stderr output: command: 'sh .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh"' .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh: line 5: 8996 Trace/BPT trap: 5 "/Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease" @"rebuild.flags" > "rebuild.log" 2>&1 Failed to run REBUILD Sorry: Failed to run REBUILD...see log file in .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log Sorry: mr_rosetta failed... Sorry routine failed Please see log file for full error message *In the rebuild logfile:* dyld: lazy symbol binding failed: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib Has anyones experienced this error? Cheers, Rhys -- Dr Rhys Grinter Sir Henry Wellcome Fellow Monash University +61 (0)3 9902 9213 +61 (0)403 896 767

4 4

Problem refining structure, error message
by Natalia Ketaren 22 Feb '16

22 Feb '16

Hello, I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8” I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

6 7