August 2008 - phenixbb - phenix-online.org

'ordered solvent' switch error (AssertionError)
by Jonathan Elegheert 22 Aug '08

22 Aug '08

Dear Phenix developers, since downloading the latest CCI Apps software release version (2008_08_09_0053), I keep running into this same error (AssertionError) when turning on the 'ordered solvent' switch in phenix.refine. I did not encounter this error with the 'release candidate 2' version I was running previously. Platform: RHEL4 with the Red Hat 8.0 or the Red Hat WS 3 (x86_64) binary bundles. Many thanks in advance for your help. Jonathan Elegheert, PhD student Ghent University ================== ordered solvent: location/analysis/update ================== Start model: number = 359 b_iso_min = 7.13 (limit = 1.00) b_iso_max = 56.80 (limit = 50.00) b_iso_mean = 27.85 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 1.92 (limit = 1.80) dist_sol_mol_max = 4.46 (limit = 6.00) Filtered: number = 324 b_iso_min = 7.13 (limit = 1.00) b_iso_max = 49.84 (limit = 50.00) b_iso_mean = 26.59 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 2.05 (limit = 1.80) dist_sol_mol_max = 4.18 (limit = 6.00) Traceback (most recent call last): File "/usr/local/PHENIX/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1081, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 364, in refinement_machine log = log) File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 159, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 332, in find_peaks log = self.log) File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", line 85, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2244, in electron_density_map "m_gradient") AssertionError

2 1

phenix.refine writing maps error
by Francis E Reyes 22 Aug '08

22 Aug '08

Writing refined structure to PDB file: /Users/francisreyes/Desktop/No_Sync/RBD_MOSFLM_P4_processing/ cns_P41_solution_18/RBD_P4PROCESS_18.1_refine_001.pdb n_use = 1586 n_use_u_iso = 1586 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 0 total number of scatterers = 1586 Traceback (most recent call last): File "/usr/local/phenix-1.3-rc2/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-rc2/phenix/phenix/refinement/ command_line.py", line 99, in run map_manger.write_files() File "/usr/local/phenix-1.3-rc2/phenix/phenix/refinement/ driver.py", line 1170, in write_files coeffs = self.refine_object.fmodel.map_coefficients(map_type=map_type) File "/usr/local/phenix-1.3-rc2/mmtbx/mmtbx/twinning/ twin_f_model.py", line 2205, in map_coefficients result = result.customized_copy( data = result.data()*aniso_scale ) RuntimeError: scitbx array_family range error Using version ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.3 Release tag: rc2 cctbx tag: 2008_05_25_1144 Platform: mac-ppc-osx osx-10.5.3 User: francisreyes ------------------------------------------------------------------------------- Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

3 2

ICSG 2008 Announcement Oxford Sept 20-24
by Thomas C. Terwilliger 22 Aug '08

22 Aug '08

Dear Colleagues, The ICSG 2008 International Conference On Structural Genomics is coming up Sept 20-24 in Oxford, UK. We have a terrific program lined up and I hope that you'll register now if you haven't already! I've copied the latest announcement of the meeting below. All the best, Tom Terwilliger ISGO International Conference On Structural Genomics, Oxford 2008 Web site: http://www.spine2.eu/ISGO The 5th International Conference on Structural Genomics (ICSG 2008) will be held in Oxford, UK on September 20-24th. The biennial Conference is the premier meeting for the Structural Genomics scientific community world-wide and is hosted on behalf of the International Structural Genomics Organization (ISGO) by Professor David Stuart at the University of Oxford, Division of Structural Biology. Keynote Speakers: Ian Wilson Dino Moras Chas Bountra Peter Donnelly Session Topics - ( See http://www.spine2.eu/SPINE2/ISGO/ for details) Structural genomics, systems biology and complexes Generating insight into protein function with structural genomics SG technologies: methodologies and dissemination The impact of structural genomics on treating diseases Structural determination, methods and computational tools International funding, co-operation and visions for the future Maximising impact on and integration with biology HTP methods for membrane proteins Hybrid/multidisciplinary approaches Strategies for intrinsically unfolded proteins Should we expand the protein universe or concentrate on biology? New Technologies Social program reservations closing date: August 31st (Blenheim Palace Dinner) Registration form: http://www.spine2.eu/SPINE2/ISGO/register The venue will be in the UK at the University of Oxford Examination Schools, High Street, Oxford. The Schools are in the heart of Oxford, central to all colleges, the main Oxford cultural and shopping areas and close to hotel and college accommodation. Registration is now open

1 0

(no subject)
by Thomas C. Terwilliger 22 Aug '08

22 Aug '08

Dear Colleagues, The ICSG 2008 International Conference On Structural Genomics is coming up Sept 20-24 in Oxford, UK. We have a terrific program lined up and I hope that you'll register now if you haven't already! I've copied the latest announcement of the meeting below. All the best, Tom Terwilliger ISGO International Conference On Structural Genomics, Oxford 2008 Web site: http://www.spine2.eu/ISGO The 5th International Conference on Structural Genomics (ICSG 2008) will be held in Oxford, UK on September 20-24th. The biennial Conference is the premier meeting for the Structural Genomics scientific community world-wide and is hosted on behalf of the International Structural Genomics Organization (ISGO) by Professor David Stuart at the University of Oxford, Division of Structural Biology. Keynote Speakers: Ian Wilson Dino Moras Chas Bountra Peter Donnelly Session Topics - ( See http://www.spine2.eu/SPINE2/ISGO/ for details) Structural genomics, systems biology and complexes Generating insight into protein function with structural genomics SG technologies: methodologies and dissemination The impact of structural genomics on treating diseases Structural determination, methods and computational tools International funding, co-operation and visions for the future Maximising impact on and integration with biology HTP methods for membrane proteins Hybrid/multidisciplinary approaches Strategies for intrinsically unfolded proteins Should we expand the protein universe or concentrate on biology? New Technologies Social program reservations closing date: August 31st (Blenheim Palace Dinner) Registration form: http://www.spine2.eu/SPINE2/ISGO/register The venue will be in the UK at the University of Oxford Examination Schools, High Street, Oxford. The Schools are in the heart of Oxford, central to all colleges, the main Oxford cultural and shopping areas and close to hotel and college accommodation. Registration is now open

1 0

Re: [phenixbb] cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 22 Aug '08

22 Aug '08

Hello Nat, thanks for your suggestions. Yes, I have used these tricks before, but sadly, the cci_apps build system ignores them completely. As far as I can see, there is no "central" place to set these variables, and the component packages behave differently. The cleanest way to go would be to just correct the syntax problems. Until recently, cci_apps was available as a precompiled irix package (and I think it was mipspro), so maybe one of the developers could comment on the specifics of this compilation. Thanks Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ----- Original Message ----- From: Nat Echols <NEchols(a)lbl.gov> Date: Friday, August 22, 2008 4:57 pm Subject: Re: [phenixbb] cci_apps on irix ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

1 0

phenix.pdbtools
by Jianghai Zhu 20 Aug '08

20 Aug '08

Hi, I am trying to use phenix.pdbtools to calculate the geometry statistics for a model from Rosetta. "phenix.pdbtools --show-geometry- statistics foo.pdb" stopped with a message "Sorry: Number of bonds with excessive lengths: 707". Anybody know what happened there? Thanks. -- Jianghai

2 1

placing ligands in coot with phenix.elbow output
by Feldman III, George Franklin 20 Aug '08

20 Aug '08

Hi all, I am having difficulties with my ligand. My ligand is an FMN (flavin mononucleotide) and its pdb file was originally created using PRODRG. I used the DRGFIN.PDB output file to run elbow (phenix.elbow DRGFIN.PDB --opt). The output contains hydrogens, which as we all know do not work well with coot. So when I try to place my ligand in its correct position and save the coordinates in coot, I get an error of duplicated atom labels when trying to merge the molecule to the ligand using phenix.refine. I tried using the command "phenix.elbow DRGFIN.PDB --opt --write-hydrogens=False" but phenix told me that last command doesnt exist (although its posted on the web page). Manually changing the atom names will affect both the connectivity and the cif file (I think), so it is an option I would rather avoid. Is there a way around all of this? Best Regards, George (Trey) Feldman

3 2

Re: [phenixbb] [phenix] generate r free flags in phenix.refine not obeying high resolution limit?
by Pascal EGEA 20 Aug '08

20 Aug '08

Hi All, Following Pavel's answer to Francis Reyes, I have a very basic question about this too. What is a good distribution of reflections and what are thin bins of resolution to ensure correct ML estimations? Are there any basic statistical rules that should be considered. Thanks Pascal Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

2 1

generate r free flags in phenix.refine not obeying high resolution limit?
by Francis E Reyes 20 Aug '08

20 Aug '08

Hi all When generating R-Free flags from phenix refine, flags are generated all the way to the limit of the data. However, shouldn't flags be generated up to the limit of the data if specified via refinement.input.xray_data.high_resolutio n ? If not, are the statistics for R/Rfree matching to high resolution data that may be suspicious ? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

3 3

(no subject)
by Sudharsan Sridharan 20 Aug '08

20 Aug '08

Hi all, A quick question about extracting info/preparing pdb file for deposition.......... I've got a pdb file after refinement using phenix 1.3b. I was wondering if there is a way to prepare this file / format this the same way as in 1.3 final where we get "REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP" and REMARK 3. i'm already running refinement 1.3 final with the same parameters just to quickly compare the resulting refined files/numbers. I guess I could do it manually but curious if there is an easier way using 1.3 final. thanks, Sid.

2 1