- phenixbb - phenix-online.org

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 23 Aug '08

23 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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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

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(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

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

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phenix.pdbtools
by Jianghai Zhu 21 Aug '08

21 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

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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

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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

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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

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(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.

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Resolution cutoffs. Always debated?
by Francis E Reyes 20 Aug '08

20 Aug '08

I need to put this in front of (this) crystallographic community. What are the criteria for cutting a resolution for data reduction ? Rmerge, I/sig, mean I/sig, completeness... more? I once believed that I/Sig (not averaged) greater than 2 was the cutoff, but I've read online (particularly http://www.mail-archive.com/[email protected]/msg02576.html) that this is no longer the case because of maximum likelihood. I would love to know why this is the case as well as poll the community on how they cut off their data. 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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Autobuild builds more residues after MR?
by Francis E Reyes 19 Aug '08

19 Aug '08

Perhaps a silly question, but suppose after MR, there is additional density to be built (say, another molecule). Will the autobuild after mr build into this new density? 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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ALS user meeting
by Peter Zwart 18 Aug '08

18 Aug '08

Dear All, I would like to draw your attention to this years ALS user meeting, held from October 13-15. In particular, the workshop titled "Recent advances in the automation of protein crystallography" might be of interest to the protein crystallographic community. The workshop consists of a series of short talks and a hands-on session in which various developers and beamline staff will demo latest developments on their beamlines. Scheduled speakers include: Gyorgy Snell (Takeda SD) Aina Cohen (SSRL) Jay Nix (ALS beamline 4.2.2) Babu Pothineni ( GMCA cat, APS) Scheduled Demonstrations are (tentative titles only) : * Efficient screening and data collection using Mini & WebIce (Bl. 5.0.n) Peter Zwart, John Taylor & Nick Sauter * Data collection @ 4.2.2 Jay Nix * SSRL & Webice Aina Cohen * Automated structure solution with PHENIX P. Afonine * Elves & 8.3.1 J. Holton Detailed workshop information can be found at http://bcsb.als.lbl.gov/wiki/index.php/ALS2008_Workshop Other workshops of interest held during the ALS user meeting can be found here: http://www-als.lbl.gov/als/usermtg/workshops.html Registration is now open for all participants: http://www-als.lbl.gov/als/usermtg/index.html Greetings Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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sharing the ext_ref_files between multiple installations
by Ben Eisenbraun 18 Aug '08

18 Aug '08

Howdy, I'm wondering if it's possible for me to put the ext_ref_files directory into a shared location and then symlink that directory into multiple PHENIX installations to save some disk space. Are the files specific to a particular PHENIX version? Or to a specific CPU architecture? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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anomalous difference map calculation option in phenix.refine
by Pavel Afonine 18 Aug '08

18 Aug '08

For many of you who asked for anomalous difference map calculation option in phenix.refine: this is fixed and available in just announced PHENIX release. Pavel.

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MemoryError
by Yingjie Zhou 18 Aug '08

18 Aug '08

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PHENIX 1.3 Available
by Paul Adams 18 Aug '08

18 Aug '08

======================================================================== ===== PHENIX 1.3 Release ======================================================================== ===== The PHENIX developers are pleased to announce that the 1.3 general release version of PHENIX is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ This version of PHENIX includes tools for: - Assessing data quality (phenix.xtriage) - Includes the detection of twinning, tNCS, and missed symmetries - Automated structure solution (phenix.autosol) - Combines automated substructure solution (phenix.hyss) with phasing (Phaser/SOLVE), substructure completion, phase improvement (RESOLVE) and fast initial model building (RESOLVE) - Automated molecular replacement (phenix.automr) - Maximum likelihood molecular replacement with Phaser - Automated protein and DNA/RNA model building/rebuilding (phenix.autobuild) - Combines automated model building (RESOLVE), phase improvement (RESOLVE) and structure refinement (phenix.refine) - Automated ligand fitting (phenix.ligandfit) - Fitting a known ligand or screening against a library of the 200 most common ligands - Structure refinement (phenix.refine) - Maximum likelihood targets, simulated annealing, TLS, constrained occupancy refinement, f'/f'' refinement, water picking, anisotropic B-factor refinement, twinned refinement, automatic treatment of alternate conformations, and joint refinement against X-ray and neutron data - Generation of ligand coordinates and restraints (phenix.elbow/ phenix.reel) - Input formats include SMILES and PDB - Restraints can be manipulated with the phenix.reel GUI Full documentation is available here: http://www.phenix-online.org/documentation/ There is a PHENIX bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium. The development of PHENIX is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. ======================================================================== ===== PHENIX 1.3 Release ======================================================================== ===== -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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HL coefficients from phenix.refine?
by William Scott 16 Aug '08

16 Aug '08

Is there a simple way to output HL coefficients in refinement, rather than just map coefficients? William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/

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Re: [phenixbb] Neutron exchangeable hydrogen/deuterium positions diverge
by Anna S Gardberg 15 Aug '08

15 Aug '08

Hi, Pavel. That's good to know. (Not pressure you, but) any idea roughly when that will be? -Anna On Thu, Aug 14, 2008 at 5:32 PM, Pavel Afonine <PAfonine(a)lbl.gov> wrote: > Hi Anna, > > Are they very different? I can easily change the code so phenix.refine makes > them identical. The question is do we really need it? I'm not arguing but > just asking. > > > A quick sampling of a handful of residues showed that the separation > at SER and THR HG/DG positions ranged from 0.37 to 1.2 Angstroem. It > seems to me that those values are too high and that there does need to > be a way to constrain them to (or at least restrain them toward) zero. > The separation at the amide positions was much less - 0.04-0.06 > Angstroem. > > > OK, I will add an option to do this. It will appear in one of the next > PHENIX releases. > > Please let me know if you have any other questions or problems! > > All the best, > Pavel. > >

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Neutron exchangeable hydrogen/deuterium positions diverge
by Anna S Gardberg 14 Aug '08

14 Aug '08

Hello, PhenixBB. I am doing joint x-ray/neutron refinement of a hydrogenated protein crystal soaked in D2O buffers, and I've run into a problem with refinement. I hope you can help. I used phenix.ready_set to add deuterium atoms to the exchangeable hydrogen positions. I ran a perl script to set the initial occupancies of those to 0.5 H and 0.5 D (they had been output as 1.0). When I ran phenix.refine with riding hydrogen positions or with individual hydrogen positions, the H and D atoms refined to different positions. How can I constrain the H and D positions to be identical? Regards, Anna Gardberg -- Anna Gardberg Research Associate, Postdoctoral Center for Structural Molecular Biology Oak Ridge National Laboratory Bldg. 4500S, M/S 6142 Oak Ridge TN 37831-6142 phone: 865-576-2173

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phenix.twin_map_utils AssertionError
by hari jayaram 14 Aug '08

14 Aug '08

Hi I am trying to run the following command phenix.twin_map_utils data.file=cy_p10_2_28.1_unique1.mtz model.file=cy_p10_2_28.1.pdb obs_labels=F_p10-2,SIGF_p10-2 free_flag=FreeR_flag When I run phenix.twin_map_utils from phenix version 1.3 final or from the newest cci_aps. I get the following AssertionError ( see below). I think my mtz file is kosher because phenix.refine with the twin_law option handles it well and I can refine with a twin law. Is there something wrong in the syntax or the file. I am attaching the log file with the Assertion Error to this email. Thanks for your help Hari Overall and bulk solvent scale paranmeters and twin fraction estimation ======================================================================= Traceback (most recent call last): File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py", line 306, in run out=log) File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 946, in __init__ assert self.f_obs.indices().all_eq( self.free_array.indices() ) AssertionError

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