- phenixbb - phenix-online.org

Re: [phenixbb] sugar links
by Ralf W. Grosse-Kunstleve 03 Sep '08

03 Sep '08

Hi Morten, > Why isn't it included in the standard set btw? Sorry, too many bigger things to take care off right now. But Garib told me he'll move the monomer library to a Google source server, which should make it much more practical to collectively work on changes like the one you're requesting. Ralf

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Re: [phenixbb] Real Space R value
by Thomas C. Terwilliger 03 Sep '08

03 Sep '08

Hi Matthew, You can also use phenix.get_cc_mtz_pdb with a ligand...it should treat the ligand as a single residue. Mark also asked offline about alternate conformations...here is my answer to that: If there is only on N for each residue, it will average over all atoms in all conformations. If there are multiple N atoms, and all atoms for each conformer are grouped, it will write out the residue twice. If there are multiple N atoms and they are interspersed, it will give an incorrect answer (it will write out the residue twice but the cc values will not be for the two conformers). All the best, Tom T > Hi, > Yes, you can use phenix.get_cc_mtz_pdb (see phenix.doc) > > But I wonder if there is a way to get CC value for a ligand or a metal > ion too ?? > > Nigel ??? > >> Date: Tue, 2 Sep 2008 13:18:59 -0400 >> From: "nih\mayerm" <mayerm(a)mail.nih.gov> >> Subject: [phenixbb] Real Space R value >> To: phenixbb(a)phenix-online.org >> Message-ID: <FEAAD2DC-1906-4194-881B-CA83B48E8043(a)mail.nih.gov> >> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed >> >> >> Is it possible to calculate a list of Real Space R values for >> structures refined with phenix.refine ? >> If so advice on how to do this would be greatly appreciated. >> >> Thanks - Mark Mayer >> >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] Real Space R value
by mathieu Coincon 02 Sep '08

02 Sep '08

Hi, Yes, you can use phenix.get_cc_mtz_pdb (see phenix.doc) But I wonder if there is a way to get CC value for a ligand or a metal ion too ?? Nigel ??? > Date: Tue, 2 Sep 2008 13:18:59 -0400 > From: "nih\mayerm" <mayerm(a)mail.nih.gov> > Subject: [phenixbb] Real Space R value > To: phenixbb(a)phenix-online.org > Message-ID: <FEAAD2DC-1906-4194-881B-CA83B48E8043(a)mail.nih.gov> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > Is it possible to calculate a list of Real Space R values for > structures refined with phenix.refine ? > If so advice on how to do this would be greatly appreciated. > > Thanks - Mark Mayer > >

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PX beamtime application deadline Sept 3rd!
by Peter Zwart 02 Sep '08

02 Sep '08

Dear All, The deadline for user proposals for PX beamtime at the ALS has been extended to September 3, 5pm pacific time. See my previous email for details. Thanks Peter 2008/8/29 Peter Zwart <PHZwart(a)lbl.gov>: > Dear All, > > The deadline for general user proposals for PX beamtime at the ALS is > comming up soon! At the BCSB, we have 5 beamlines for which you can > apply for beamtime. At the Berkeley Center for Structural Biology > (BCSB) we have recently completed a number of upgrades: > > Sector 8: Recent improvements include: > > * A high-accuracy microdiffractometer on BL 8.2.1, allowing for > centering and viewing of very small crystals > * Robot automounters which can increase the screening throughput > at the beamlines, and will allow for the implementation of remote data > collection > * A new large format (315mm active surface area) CCD detector on > BL 8.2.1, facilitating data collection on large unit cell crystals > > Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons > per second at 0.97 Angstrom. This wavelength is slightly above the Se > K edge making them ideal for performing Se SAD experiments. Beamline > 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons > per second, and the energy range of 5.0.2 has been extended to 17 keV, > enabling the routine use of shorter wavelengths and anomalously > scattering elements such as bromine. > > Please visit http://bcsb.lbl.gov/ for more details about the Center > and its beamlines. > > If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light > Source, please submit a General User proposal by September 1, 2008. > > To find out more, click on: > > http://www-als.lbl.gov/als/quickguide/independinvest.html > > We invite you to submit a proposal at: > > http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. > > If you have any questions or would like to request open beamtime, > please e-mail BCSBBeamtime(a)lbl.gov. > > (Please note that executed user agreements must be received by LBNL > prior to beamtime. Proprietary fees, if applicable, must be received > by LBNL at least five working days prior to scheduled beamtime.) > > > -- > ----------------------------------------------------------------- > 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 > ----------------------------------------------------------------- > -- ----------------------------------------------------------------- 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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Real Space R value
by nihmayerm 02 Sep '08

02 Sep '08

Is it possible to calculate a list of Real Space R values for structures refined with phenix.refine ? If so advice on how to do this would be greatly appreciated. Thanks - Mark Mayer

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LABIN and BLUR like options in phenix refine?
by Partha Chakrabarti 01 Sep '08

01 Sep '08

Hiya, If we use sharp for phasing, the eden_flat file has multiple columns at the end. I was wondering if it is possible to tell the program which ones to use other than having to use CAD.. and, if the FOM is suspected to be too high, Blur it.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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PX beamtime application deadline Sept 1st!
by Peter Zwart 29 Aug '08

29 Aug '08

Dear All, The deadline for general user proposals for PX beamtime at the ALS is comming up soon! At the BCSB, we have 5 beamlines for which you can apply for beamtime. At the Berkeley Center for Structural Biology (BCSB) we have recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1, allowing for centering and viewing of very small crystals * Robot automounters which can increase the screening throughput at the beamlines, and will allow for the implementation of remote data collection * A new large format (315mm active surface area) CCD detector on BL 8.2.1, facilitating data collection on large unit cell crystals Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light Source, please submit a General User proposal by September 1, 2008. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) -- ----------------------------------------------------------------- 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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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 27 Aug '08

27 Aug '08

Dear Users, The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for October/November/December 2008 allocation period, proposals must be submitted by Sept 1, 2008. The deadline for CC proposals for the time period January/February 2009 will be November 15, 2008. Regards, Banumathi Sankaran

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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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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 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

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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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