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Re: [phenixbb] sigma cutoff
by Kay Diederichs 30 Nov '09

30 Nov '09

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

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Re: [phenixbb] Confused by the output from Phenix autobuild jobs
by Thomas C. Terwilliger 30 Nov '09

30 Nov '09

Hi Serah, You are right that the coefficients that you want for a difference map are not present in the overall_best_refine_map_coeffs.mtz file. The coefficients in that file (labelled FP PHIM) are the same as 2FOFCWT PH2FOFCWT from the refinement output, but there are no difference map coefficients. I will change this. In the meantime, I would do this after the end of autobuild: phenix.refine AutoBuild_run_1_/overall_best.pdb \ AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz and then you will have your map coefficients. >> I'm still wondering about the overall_best_*.* outputs - are these the >> really final output, or do we go for cycle_best_3.* series? The overall_best_xxx files are copied from the cycle_best_xxx files which are copied from the original files, all of which are in the TEMP0/ subdirectory. Thanks for pointing out that the difference coefficients are not present in the autobuild map file. I will fix the output to have the original refinement map file available. All the best, Tom T

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alternate conformation
by subhash bihani 25 Nov '09

25 Nov '09

Hi, I am refining a structure with ligand in alternate conformations. I tried giving them A and B, it worked. but I feel that this doesnot make interactions between alternate conformations absolutely zero. Is there any command in phenix similar to Igroup statement in CNS which can be used for such cases. Regards subhash -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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R-free rules
by Bryan W. Lepore 25 Nov '09

25 Nov '09

in the phenix.reflection_file_editor gui not sure i understand this: [x] Extend existing R-free array(s) ... [R-free flags generation] <--+ | | | | +-if this is checked, then do NOT check "Generate R-free flags" in here ... because "extend" is not the same as "generate", right? ... and thanks for the help before. -bryan

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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 23 Nov '09

23 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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