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Age Concern edition of the Computing Commission and Teaching Commission newsletter
by Ralf W. Grosse-Kunstleve 24 Nov '09

24 Nov '09

Posted on behalf of Lachlan Cranswick: The Computing Commission and Teaching Commission has produced a joint November 2009 newsletter on the theme of "Age Concern", which deals with issue concerning "the slow march towards retirement of the major generation of crystallographic programmers", as further explained by David Watkin within the newsletter. http://www.iucr.org/resources/commissions/crystallographic-computing/newsle… or via http://www.iucr.org/resources/commissions/crystallographic-teaching/newslet… --------------------------- This issue's articles include : - the latest background and information from the UK based EPSRC funded Age Concern Project. - history and science within the Caltech based CRYRM single crystal suite; DIMS - Direct methods In Multidimensional Space software; Crunch 1.5 Direct Methods Software; the Glasgow based GX single crystal suite; the Italian based CAOS structure refinement software; Ton Spek's Platon; and a list of programs archived at Armel Le Bail's Crystallography Source Code Museum. - experience in conversion of large crystallographic Fortran-77 to C++; as well as the place of the Quick and Dirty Crystallographic Computer Program - Historical group photographs from some of the Crystallographic Computing and Teaching School of the 1970's. - Archived manuals and source code from the above mentioned software. - Teaching material of Isabella L. Karle, as she presented at the 1978 Erice School on Direct Methods for Solving Crystal Structures - A reprint of the The Analytical Theory of Point Systems (1923) by J. D. Bernal (1901-1971) Further Computing Commission newsletters are intended on theme of Age Concern : capturing the history and the crystallographic science behind past and present Small Molecule, Powder Diffraction, Protein and other crystallographic software. Submissions on this topic are welcome and encouraged. - Lachlan Cranswick ( lachlan.cranswick(a)nrc.gc.ca )

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Confused by the output from Phenix autobuild jobs
by Serah Wangari 24 Nov '09

24 Nov '09

Dear Phenix users, I have run a number of Autobuild jobs using the Phenix GUI and in all cases, I'm not sure what output I should proceed with to the next step. - The first job was for rebuilding a loop section in the model (rebuild-in-place) - As far as I can remember, there was no mtz generated from this job, I had to generate map coefficients with the overall_best pdb and an old mtz using another refinement program. Did I miss something during the job input step, so that no mtz was generated, or how would I proceed in such a case? - The next job involved rebuilding the whole model (rebuild-in-place) - in this case, I took the overall_best pdb, but when I tried to open the overall_best_refine_map_coeffs.mtz in coot, I got this error that coot failed to find F/Phi columns in the mtz file. Then I checked in the TEMPO directory, and I managed to open a random mtz from one of the refinement cycles with coot, but I wasn't confident building into that, so again I had to generate map coefficients using overall_best pdb and an old mtz in another program. - The other job was rebuilding (rebuild-in-place) another model with composite maps generation - Here, in addition to the 12 mtz and pdb files from the 12 omit regions, I got resolve_composite_map.mtz I should assume as the only final output; and no final pdb. Again, this mtz file doesn't have the F/Phi columns as I got the same error as above in coot. I'm not sure how to proceed with this mtz...... I would really appreciate if someone could point me to the right direction or at least direct me to some literature where the output from Phenix autobuild jobs is explained - as I haven't come across such info yet. Thank you in advance, Serah --

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Clean Jobs
by tea.pavkov＠uni-graz.at 24 Nov '09

24 Nov '09

Dear all, I would have a general question - how can I clean the Jobs (in the Job history list and all corresponding directories) in the new GUI? Thank you in advance! Best regards, Tea ----------------------- Dr. Tea Pavkov-Keller KF Uni Graz, ZMB Structural Biology Group Humboldtstr. 50/III 8010 Graz Austria

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Problem installing on Leopard PowerPC G5
by Satpal Virdee 23 Nov '09

23 Nov '09

Hi, I am trying to install the latest 1.5-2 official release on an iMac PowerPC G5 running OSX 10.5.8. During installation I get the error: " Relocating Python framework. . . /usr/bin/install_name_tool: object: libwx_mac-2.8.0.5.0.dylib malformed object (unknown load command 20) Error: see /Users/Sat/Downloads/phenix-installer-1.5-2/build-binary/ mac-ppc-osx/cpemac406-18/log/binary.log for details " Inspection of the binary.log files reveals this: " libfreetype.6.3.10.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/ base/lib/libfreetype.6.3.10.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.3.10.dylib libfreetype.6.dylib libfreetype.6.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/ lib/libfreetype.6.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.dylib libfreetype.dylib libfreetype.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/ libfreetype.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype.dylib libwx_mac-2.8.0.5.0.dylib fix_mac_python: caught error - exiting. " Any help would be most appreciated. Regards, Satpal

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baton build in coot
by Raja Dey 22 Nov '09

22 Nov '09

Dear Friends, How does CA ZONE > MAIN CHAIN under 'other modeling tools' in coot work? I was trying to rebuild main chain atoms for 3 residues(8,9,10) using CA ZONE > MAIN CHAIN. when I click on one atom in residue 8 and then one atom in residue 10, it failed with a message that says the zone is too short. I increased the zone to 5 residues, still same failed message. Also, is it possible to move an atom in coot? Thanking you in advance for your reply. Raja

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phasing power value in Autosol/Autobuild
by vennila Natesan 19 Nov '09

19 Nov '09

Dear all... I need toknow the phasing power value for my solved structure. Where can i find it out in the output files of autosol and autobuild? I am using phenix1.14.4b and also i need to know the weighted mean phase errors vs resolution. Thanking you.

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I vs F data input
by gerwald jogl 18 Nov '09

18 Nov '09

Hi All, A quick question about diffraction data input. I just noticed that phenix.refine uses Imean/SIGImean and converts these by default in my refinements. Is this the preferred way or would it be better to use F/SIGF (after CCP4)? Thanks, Gerwald

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external ncs reference structures?
by Cathy Lawson 18 Nov '09

18 Nov '09

Dear Phenix developers, We are finishing up refinement of some multiprotein-DNA complex structures at 3-3.5 A resolution and I am wondering if it would be possible with phenix.refine to supply one or more external sets of coordinates from higher-resolution determinations to serve as the ncs references. If so what would be the best way to set this up? thanks, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson(a)rutgers.edu http://roma.rutgers.edu **********************************

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Mac OSX Phenix GUI
by Miguel Ortiz Lombardia 18 Nov '09

18 Nov '09

Hi, This is a question/request to the phenix developers. Are there any plans to make the new phenix GUI to use an X11 python interface instead of the Aqua one? The reason I ask is that we use Mac OSX servers for calculations here and an X11 interface would be a lot more appropriate for this configuration. That way users could export the GUI to their local workstations. As it is implemented now this use of the GUI is impossible on Mac OSX. Before someone makes the suggestion: Remote Desktop simply allows to share the only Aqua desktop that the server can produce, that is, only one user can access the Aqua desktop, whether remotely or locally. We would be happy to test any X11 version you might be willing to develop. Thanks for your great software, which we can use anyway from the command line :-) Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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Phaser output and error messages
by Ian Stokes-Rees 17 Nov '09

17 Nov '09

I'm having some discussion with a colleague about phaser output (we're using Phaser 2.1.4). We haven't been able to find any documentation which can clarify our situation, and I'm hoping someone on the list can help answer these questions. I should mention that I am relatively new to Phaser. 1. PHASER.sol files: Which "SOLU SET" does Phaser consider to be the best? The first or the last? Or the one with the highest LLG, wherever that may be? In our experience of running Phaser over several MTZ files with a range of models the best Phaser solution has always been the first, and this has had the highest LLG. Note: this is with "untuned" Phaser settings for identity, solvent fraction, or number of search models in ASU -- our goal is to do a first run with "generic" settings for these over a larger set of models, then (from TFZ and LLG scores) select a subset for which we will tune Phaser parameters and PDB search model variations. 2. If we are right that the first "SOLU SET" entry is indicative of the potential for the search model to form a good MR candidate, then is it the case that the first entry is the first Phaser solution that is computed? Or is the PHASER.sol file a sorted list output at the end of the run? From my reading of the documentation it is output in order of computation, and *for our purposes* (if my first statement in this question is correct) Phaser can stop after it outputs this first solution. Is there some way to tell Phaser to stop after the first solution is output? I realize that this doesn't sound like it makes sense (how could Phaser know to pick the best solution first, and even if it could, why would it ever continue past this point), however I ask because we have put a 10 minute timeout into our Phaser runs and we have many situations where we get a timeout but PHASER.sol has already been generated and the best LLG solutions are output first. It leaves me wondering why it didn't just stop on its own after outputting the first result instead of being aborted by our (external) timeout that terminates the process? 3. PHASER.sol files: For single domain search models, we usually get output of the form: SOLU SET RFZ=4.5 TFZ=5.2 PAK=0 LLG=14 LLG=14 SOLU 6DIM ENSE model1 EULER 242.049 45.040 326.088 FRAC -0.09425 0.50268 0.42575 however we see three variations: i) No LLG: SOLU SET RFZ=3.1 TFZ=5.0 PAK=0 SOLU 6DIM ENSE model2 EULER 59.983 69.335 319.701 FRAC -1.17131 -0.70030 0.23150 ii) One LLG: SOLU SET RFZ=3.7 TFZ=4.6 PAK=0 LLG=25 SOLU 6DIM ENSE model3 EULER 293.943 128.068 332.147 FRAC 0.06273 0.13175 0.25054 iii) Two LLG entries, but with different values: SOLU SET RFZ=3.8 TFZ=4.1 PAK=0 LLG=21 LLG=20 SOLU 6DIM ENSE model4 EULER 278.058 129.347 33.292 FRAC 0.28446 0.29011 -0.07986 4. Occasionally we get an error that we don't understand: FATAL RUNTIME ERROR: No scattering in pdbfile model1.pdb What does this mean? Is there a problem with the PDB file? We can't see anything obvious in the ones which produce this error. Thanks, Ian -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org

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