- phenixbb - phenix-online.org

map calculation
by Chen Chen 27 Aug '08

27 Aug '08

Dear all, I am having a question about map calcultation. I want to calculate a 2mFo-DFc map and a mFo-DFc map to 2.0 angstrom from xxx.pdb and yyy.mtz, and zzz.cif should be supplied. Unit cell dimension and symmetry information is in the mtz file. It seems that phenix.maps can do the job, but I did not find a good document on how to run it. In its help information, a parameter file is needed. I tried do use parameter file for refinement, which has been successfully used for phenix.refine, and I ran the command phenix.maps --unused_ok yyy.mtz xxx.pdb refine.param but phenix.maps report the error Traceback (most recent call last): File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/command_line/maps.py", line 7, in <module> maps.run(args=sys.argv[1:]) File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 173, in run log = log) File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 214, in __init__ self.data = utils.determine_data( AttributeError: 'module' object has no attribute 'determine_data' Does anyonw know what I should do to get the maps? Thanks Chen -- Chen Chen, Ph. D., Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 Office Phone: 240-314-6122

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MTZ file
by YS. Chung 27 Aug '08

27 Aug '08

Hi all, I have a simple question about the output mtz file from phenix.refine. When I look at the mtz file, it says *********************************************************** DO NOT USE THIS FILE AS INPUT FOR REFINEMENT! Resolution and sigma cutoffs may have been applied to FOBS. *********************************************************** If I have not applied either resolution or sigma cutoffs to FOBS, does that mean that this mtz file is ok to be used for the next round of refinement? Thank you, Yu Seon Chung

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Dry shippers
by Peter Zwart 25 Aug '08

25 Aug '08

Dear all, Due to the presence of residual liquid nitrogen in dry shippers 'steaming' out of a tipped-over dewar on a Fedex dock, we (PX-ers in the ALS) have been placed under some scrutiny with regards to dry-shipping dewars. In particular, I am interested in how people empty their dewars/pucks/vials and prepare them for dry-shipment and how they and/or their shipping department checks if the dewars are empty indeed. Cheers Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Refining with NCS
by Francis E Reyes 25 Aug '08

25 Aug '08

All I have 4 molecules in my ASU and I had phenix pick out my NCS operators automatically. Do a round of refinement, load 2fofc maps into coot and ask to calculate NCS Maps (Calculate -> NCS Maps). I have three new maps mapping a single chain onto the other chains (3) and an NCS average map. I look at some of the NCS maps and the question is should the model (all the chains) match to every NCS map? In my set of 3 maps, the model fits one map (independent of chain) but seems offset in the other two maps. Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to). 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

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anisotropic refinement and hydrogens in coot.
by Mark Collins 25 Aug '08

25 Aug '08

Two hopefully quick questions; 1) The phenix.refine documentation has a section 'Refinement at "higher than medium" resolution - getting anisotropic'. I have a 1.4A structure that clearly falls into this category, I've added riding hydrogens and now I'd like to try anisotropic ADPs. Is there a way, to list all residues (preferably in phenix selection format) that have "relatively small isotropic B-factors ~5-20A**2 of so."? 2) The output.pdb file from phenix.refine is I think the pdb v3.0 format. Is there an option or apps to convert to v2.3, within phenix rather using remediator (duke)? Coot still uses v2.3 files, which is fine until hydrogens are added to a pdb, because the nomenclature has changed. RSR in coot causes these 3.0 named hydrogens to fly off the residue into surrounding density. Thanks in advance, Mark

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Re: [phenixbb] cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 25 Aug '08

25 Aug '08

Hello Ralf, I have now tried to compile the cctbx version of May 25th (which was the latest version with an official IRIX build). It gives me the very same type of error which I have seen with the latest cci_apps: -------- Declaration is incompatible with function template "boost::basic_format<Ch, Tr, Alloc> &boost::io::detail::feed(boost::basic_format<Ch, Tr, Alloc> &, T)" (declared at line 52 of "/usr/local/archive/cctbx/2008_05_25/cctbx_sources/boost/boost/format /internals_fwd.hpp"). io::detail::feed (basic_format<Ch2, Tr2, Alloc2>&, T); --------- This means that probably there always have been certain changes to be made for the code to compile under IRIX/Mipspro. Could somebody maybe tell me the email address of the person who actually did the last IRIX build, or just forward my message accordingly? Thanks a lot! 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: "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov> Date: Sunday, August 24, 2008 12:41 pm Subject: Re: [phenixbb] cci_apps on irix > Hi Oliver, > > You can get the boost directory via these cctbx bundles: > http://cci.lbl.gov/cctbx_build/ > Click on the date/time tag for the cci apps version you had > previously, or if you don't know, go back one by one. > BTW: there is no need to delete cci apps or phenix versions. > Simply don't source the old setpaths or phenix_env and the > old version is "virtually not there (tm)". > > Ralf > ------------------------------------------------------------------- ------------------------------------------------------------------- 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 ------------------------------------------------------------------- -------------------------------------------------------------------

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Re: [phenixbb] cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 24 Aug '08

24 Aug '08

Hello Ralf, thanks a lot for Your suggestions. Yes, I have thought about that, comparing with the older version to fix the differences. Unfortunately, I was brave enough to delete my previous (precompiled) version before I realized that IRIX support has been dropped in the meantime !!! The cci_apps download area does not provide an obvious possibility to download an older version (the cci_apps packages don't have version numbers anyway). But maybe somebody could provide a link to the latest sgi-compatible version (sources and binary package, if possible)?? That would be great! If these minor problems can be solved, it should be no problem to compile the main phenix package ;)) Cheers 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: "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov> Date: Sunday, August 24, 2008 3:48 am Subject: Re: [phenixbb] cci_apps on irix > > I am just compiling the latest cci_apps package for the IRIX > > platform. I know this is unsupported, but since the package is very > > self-contained, I would not expect major problems with the > command-line > > packages (who needs a gui, anyway ;)) > > I'm just running into two issues with the boost package which are > > obviously a matter of syntax: > > The first one is a typical MIPSpro quirk and would be easy to fix > (add inline to the prototype), but I'm not sure about the second one. > Unfortunately we don't currently have a MIPSpro machine I could use > to figure this out (not enough power in the room to keep that old > amp-eater running!). > Do you still have an older CCI Apps that worked on your machine? > Then you could try to replace the newer boost sources with the > older version. E.g. something like > > cd /usr/local/archive/phenix/cci_apps-1.3/cci_apps_sources > mkdir incompatible > mv boost incompatible > cp -r /usr/local/archive/phenix/cci_apps-that- > worked/cci_apps_sources/boost . > cd .. > rm cci_apps_build/.sconsign.dblite # like make clean; could be > important ./cci_apps_install_script.csh > > Ralf > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > ------------------------------------------------------------------- ------------------------------------------------------------------- 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 ------------------------------------------------------------------- -------------------------------------------------------------------

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cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 24 Aug '08

24 Aug '08

Hello, I am just compiling the latest cci_apps package for the IRIX platform. I know this is unsupported, but since the package is very self-contained, I would not expect major problems with the command-line packages (who needs a gui, anyway ;)) I'm just running into two issues with the boost package which are obviously a matter of syntax: 1st: ----- Function function "boost::python::api::object_base::~object_base" is redeclared "inline" after being called. inline api::object_base::~object_base() ^ ----- 2nd: ----- Declaration is incompatible with function template "boost::basic_format<Ch, Tr, Alloc> &boost::io::detail::feed(boost::basic_format<Ch, Tr, Alloc> &, T)" (declared at line 52 of "/usr/local/archive/phenix/cci_apps-1.3/cci_apps_sources/boost/boost/ format/internals_fwd.hpp"). io::detail::feed (basic_format<Ch2, Tr2, Alloc2>&, T); ^ ----- I have attached the complete output for your reference. Maybe these problems can be corrected easily. In fact, all this may be a matter of the mipspro compilers being more strict about syntax than gcc. But how to tell the install script to use gcc??? There doesn't seem to be a standard way to provide general compilation options... Just renaming the cc binaries makes the python configure script to switch to gcc without complaints, but other packages (scons if I remember correctly) still explicitly check for mipspro ?! Any ideas how to resolve this? 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 ------------------------------- ------------------------------------------------------------------- ------------------------------------------------------------------- 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 ------------------------------------------------------------------- -------------------------------------------------------------------

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'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

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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

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