July 2009 - phenixbb - phenix-online.org

Average B-factor and ML error
by Leo Sazanov 15 Jul '09

15 Jul '09

Hi, phenix.refine outputs "WILSON B" value into PDB header after refinement, which is not the same as average B-factor of all the atoms in the structure, and not exactly the same as Wilson B-factor from SCALA scaling. How exactly is Wilson B-factor for phenix header calculated and would it be possible to output there also the average B-factor of all the atoms in the structure? Also, deposition into PDB requires only Luzzati coordinate errors, while phenix produces only ML based ones. Presumably ML estimate is better than Luzzati?, but it looks like often people just ignore PDB input for errors. It seems that it would it be useful in future to have ML option in the PDB submission process? Or should Phenix produce Luzzati errors as well? (I know that one can calculate av. B-fac in other programs or ask PDB to add some data to the deposition, but if the idea is to streamline the process...) Thanks, -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915 -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Anyone have a phenix.resolve script for after Phaser ?
by Phil Jeffrey 15 Jul '09

15 Jul '09

Although my usual m.o. is SHELX -> SHARP I'm exploring HYSS -> PHASER -> RESOLVE to see if the maps are any more interpretable. I think I've got good scripts for the first two steps but I'm not sure about my resolve script which stands at: phenix.resolve << EOD hklin myp3_auto.mtz LABIN FP=F SIGFP=SIGF PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD hklout resolve.mtz solvent_content 0.45 seq_file myp3.pir EOD This runs, but I could not tell from delving into the documentation if this was ideal or not. Thanks Phil Jeffrey (a Luddite and not using the GUI) Princeton

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Re: [phenixbb] refine occupancy of partially overlapping ligands
by Chris Ulens 14 Jul '09

14 Jul '09

Hi, I'm trying to refine the occupancy of 2 ligands that occupy the same binding pocket in 2 *partially* overlapping orientations. Let's assume I would define the ligands in 2 separate "chains" termed A and B. Could the experts point me to the proper syntax to define the correct group restraints to refine the occupancy? Thank you. Chris +++++++++++++++++++++++++++++++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium Tel +32 16 345812 Fax +32 16 345699 Telepathy 2.69 GHz +++++++++++++++++++++++++++++++

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can't find phaser_mtz.hand.mtz?
by Pei-Chun Lin 14 Jul '09

14 Jul '09

Hi, I am the beginner of crystallography and have a 3.5A map generated by MAD method using phenix GUI. I already traced and built 2/3 of my protein. I wish to use this partial model combined with SAD to generate a new map and see if the new map can help me to deal with the rest of the structure. Does it sound reasonable to you? However, after running AutoSol. I got this error message: Failed to carry out AutoSol_score_ha_solutions: [Errno 2] No such file or directory: 'AutoSol_run_1_/TEMP0/phaser_mtz.hand.mtz' What should I do now? Can't phenix automatically calculate it? PC _________________________________________________________________ Windows Live™: Keep your life in sync. Check it out! http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_012009

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tightening geometry
by Patrick Loll 10 Jul '09

10 Jul '09

Hi, I'm a little baffled. We have a 3 Å structure, and while the R values seem OK, I'd like to tighten up the rmsd values for the geometry. However, altering wxc_scale seems to have no effect. Specifics: In a clean directory, I run the following command phenix.refine X.mtz Y.pdb Z1.cif Z2.cif Z3.cif wxc_scale=0.??? strategy=group_adp (the cif files are libraries for different ligands) When I vary wxc_scale from 0.5 to 0.005, the geometry doesn't change at all, which makes no sense to me: For wxc_scale=0.5 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.05 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.005 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 ...you get the idea. These were run with phenix-1.4-3. With phenix-1.4-56, we get subtly different r values, but the bonds and angles numbers are the same as shown above (to 3 decimal places!), and the numbers don't change upon changing wxc_scale. Am I missing something here? Is there a better way to tighten up the geometry? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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Re: [phenixbb] source of fobs for refinement after AutoSol
by Tom Terwilliger 09 Jul '09

09 Jul '09

Hi James, Yes, that is correct. However if you want...you can just go on to AutoBuild and build a new model from scratch and generate a set of free R flags there, supplying your data as data=mydata.sca. I would recommend this anyway because AutoBuild makes a much better model than AutoSol, and including the model from AutoSol doesn't necessarily help (and can make it worse if the AutoSol model is really incomplete, such as from secondary- structure-only model-building). I use the AutoSol model-building just to see if things are going well and then I throw that model away. This is also the default when you use "after_autosol=True" in AutoBuild and when you run the AutoBuild GUI after running AutoSol. It is convenient to use the data and freeR in in exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to. The key of course is: once you refine a model and want to use that model further...you must use the set of free R flags used in that original refinement from then on. If you throw away that model and start from scratch you can also make a new set of free R flags. The hexdigest REMARK in your PDB file from phenix.refine helps you make sure that this is done correctly. All the best, Tom T On Jul 9, 2009, at 8:35 AM, James Whittle wrote: > Dear Tom: > > Ok. Thanks for the quick response! > > I should run then run AutoSol again to get this file, and it will > have the HL coefficients in it? > > --James > > > On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote: > >> Hi James, >> >> As you are expecting, in AutoSol the file >> exptl_fobs_phases_freeR_flags_*.mtz normally contains the >> experimental Fobs and free R flags for refinement, along with >> phases and HL coefficients from the experimental phasing. >> >> However if an anisotropy correction is applied to the data, then by >> default no refinement is done in AutoSol and no >> exptl_fobs_phases_freeR_flags_*.mtz file is created. This is to >> ensure that refinement is not carried out against anisotropy- >> corrected data (you want to refine against the original data, and >> have phenix.refine apply an anisotropy correction as part of >> refinement). >> >> If you supply >> >> input_refinement_file=my_data.sca >> >> then my_data.sca will be used for refinement and an >> exptl_fobs_phases_freeR_flags_*.mtz will be created. Note that >> my_data.sca can be identical to your input data file if you want. >> I am guessing that in your case an anisotropy correction was >> applied to the data in this way. >> >> I hope that helps! >> -Tom T >> ps. I am thinking of changing the default to make >> input_refinement_file automatically defined if an anisotropy >> correction is applied so that you don't have to do this... >> >> On Jul 9, 2009, at 7:55 AM, whittle wrote: >> >>> Dear all, >>> >>> I have a question regarding the output of AutoSol. >>> >>> I've run AutoSol, using the data directly from scalepack as a .sca >>> file, >>> and would like to now begin refining the structure I've built. >>> >>> There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the >>> AutoSol directory. Isn't this the right file to use? Since it's not >>> there, is it proper to use the phaser_2.mtz file for phenix.refine? >>> >>> --James >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >> PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web >> site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB >> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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source of fobs for refinement after AutoSol
by whittle 09 Jul '09

09 Jul '09

Dear all, I have a question regarding the output of AutoSol. I've run AutoSol, using the data directly from scalepack as a .sca file, and would like to now begin refining the structure I've built. There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the AutoSol directory. Isn't this the right file to use? Since it's not there, is it proper to use the phaser_2.mtz file for phenix.refine? --James

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2010 Gordon Conference on Diffraction Methods
by Andrew Leslie 02 Jul '09

02 Jul '09

The Gordon Research Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine, from July 18-23, 2010. As in the past, the program will include the latest developments in methodology covering all aspects of macromolecular crystallography, from crystallisation to model refinement and validation. We are currently preparing a preliminary program for the meeting, and would welcome suggestions for particular topics (with or without speakers). Please Email your suggestions to Andrew Leslie (andrew(a)mrc-lmb.cam.ac.uk) or Ana Gonzalez (ana(a)slac.stanford.edu). Andrew and Ana

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map output by phenix.refine
by 丁玮 02 Jul '09

02 Jul '09

Hi Pavel, Thank you for responding to my question so eloquently. But there are still something confusing me. First of all, when I used coot to open the "_map_coeffs.mtz", only two maps were displayed in the window,not four? Second, how to choose the maps coefficients? In phenix documentation, we konw that any specified coefficients can be set, for example: 2mFo-DFc, 2.7mFo-1.3DFc, Fo-Fc, 3Fo-2Fc. but it do not tell us why we should choose different coefficients. Thanks a lot. dream830106

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GUI problems
by Phil Evans 01 Jul '09

01 Jul '09

Hi I've just installed the Linux 64-bit version 1.4-105 on a CentOS5 machine, and I get a lot of errors in starting up the GUI. What am I missing? Also is it possible to install both the 32-bit & 64-bit versions together: I know it works for the executables in build/intel- linux-2.6 build/intel-linux-2.6-x86_64, but does that mess up the gui? It's OK on the command line Phil

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