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Re: [phenixbb] How do I gather the pieces after AutoBuild?
by Thomas C. Terwilliger 26 Dec '07

26 Dec '07

Hi Dale, If you run AutoBuild with "rebuild_in_place=Yes" then it will keep the pieces that you have, try to rebuild them (in nearby locations), and not reassemble the molecule. Rebuilding in place is supposed to be a way to finish off your structure, and that's why it doesn't move it around. In your case, you are rebuilding in place after Phaser molecular replacement. Usually Phaser will make a compact molecule during MR, so this should not normally be a problem. I gather that in this case it didn't do so, however. With rebuild_in_place=No then AutoBuild should try and make a compact molecule. If you have NCS then it will try to make a compact molecule with NCS. All the best, Tom T > Hi all, > > I have finished my Autobuild but the resulting model has some residues > that are scattered in distant asymmetric units. Coot shows their symmetry > images where they belong, next to the rest of the protein. I could > rebuild these residues by hand in the right place, or collecte together > all the symmetry operators and write a script to gather them, but being > lazy would like a more automated solution. Surely this happens to > other people and there is a tool that solves this problem. I've read > a bunch of the web pages for AutoBuild but didn't find a solution there. > > My AutoBuild command was > > phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ > map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ > seq_file=../fmo-ct.pir \ > resolution=2.2 dmax=20 refinement_resolution=2.2 \ > cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif > \ > input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ > rebuild_in_place=Yes > > Shouldn't AutoBuild build a compact model by default? > > Dale Tronrud > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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How do I gather the pieces after AutoBuild?
by Dale Tronrud 23 Dec '07

23 Dec '07

Hi all, I have finished my Autobuild but the resulting model has some residues that are scattered in distant asymmetric units. Coot shows their symmetry images where they belong, next to the rest of the protein. I could rebuild these residues by hand in the right place, or collecte together all the symmetry operators and write a script to gather them, but being lazy would like a more automated solution. Surely this happens to other people and there is a tool that solves this problem. I've read a bunch of the web pages for AutoBuild but didn't find a solution there. My AutoBuild command was phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ rebuild_in_place=Yes Shouldn't AutoBuild build a compact model by default? Dale Tronrud

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Re: [phenixbb] autosol w/ "no merge original index"?
by Tom Terwilliger 19 Dec '07

19 Dec '07

Hi Brian, Thanks for sending me the top of your hkl file....I added some random data after that and it runs on my version just fine. Can you possibly try again with the most recent version of phenix on the web site (rc6)? Thanks! -Tom T At 01:24 PM 12/19/2007, you wrote: >phenix 1.3b of 21-10-2007 > >confusion w/ "no merge original index" data file in phenix.autosol. this >should work, right? > >caveat - the 'nmoi' hkl is actually from scala, but that usually is fine >w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on >command line. > >phenix.autosol seems to go through all the usual checks fine, then >reports (in AutoSol_run_2_/LAST.LOG): >".... > The error seems to be at line 0 > Here is what the first few lines of this file look like: > 1 > -987 > 86.052 86.052 132.608 90.000 90.000 90.000 p41212 > You have set the keywords readdenzo and unmerged > Please check whether you should have set readformatted or readtrek or >premerged >...." > >... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. > >-bryan >_______________________________________________ >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

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Re: [phenixbb] autosol w/ "no merge original index"?
by Tom Terwilliger 19 Dec '07

19 Dec '07

Hi Bryan, Yes, "No merge original index" files should work fine. This file should be converted by the autosol wizard to premerged scalepack during the run. In your case this seems to be so as the file header that is being read during the middle of the run 1 -987 86.052 86.052 132.608 90.000 90.000 90.000 p41212 is premerged scalepack. Now what does not make sense is the error message "You have set the keywords readdenzo and unmerged". I am not sure where that has come from. I just ran a SAD dataset to test this with an unmerged original index file, and it ran fine for me. If this doesn't help, could you send me (terwilliger(a)lanl.gov) your input script and datafile ( or even the first 1000 lines of the datafile) and I can try to debug it. Thanks! -Tom T At 01:24 PM 12/19/2007, you wrote: >phenix 1.3b of 21-10-2007 > >confusion w/ "no merge original index" data file in phenix.autosol. this >should work, right? > >caveat - the 'nmoi' hkl is actually from scala, but that usually is fine >w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on >command line. > >phenix.autosol seems to go through all the usual checks fine, then >reports (in AutoSol_run_2_/LAST.LOG): >".... > The error seems to be at line 0 > Here is what the first few lines of this file look like: > 1 > -987 > 86.052 86.052 132.608 90.000 90.000 90.000 p41212 > You have set the keywords readdenzo and unmerged > Please check whether you should have set readformatted or readtrek or >premerged >...." > >... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. > >-bryan >_______________________________________________ >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

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autosol w/ "no merge original index"?
by Bryan W. Lepore 19 Dec '07

19 Dec '07

phenix 1.3b of 21-10-2007 confusion w/ "no merge original index" data file in phenix.autosol. this should work, right? caveat - the 'nmoi' hkl is actually from scala, but that usually is fine w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on command line. phenix.autosol seems to go through all the usual checks fine, then reports (in AutoSol_run_2_/LAST.LOG): ".... The error seems to be at line 0 Here is what the first few lines of this file look like: 1 -987 86.052 86.052 132.608 90.000 90.000 90.000 p41212 You have set the keywords readdenzo and unmerged Please check whether you should have set readformatted or readtrek or premerged ...." ... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. -bryan

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Re: [phenixbb] MTZ intensities interpreted as amplitudes by autobuild command-line versions up to 1.3b/rc6
by Thomas C. Terwilliger 18 Dec '07

18 Dec '07

Hi again Peter, Yes, the AutoMR wizard (any version) will run correctly with input MTZ data that are intensities. However all versions up to now will pass this MTZ file on to AutoBuild without conversion to amplitudes and it will be incorrectly interpreted by AutoBuild. Note that this only applies to MTZ files. Any other source of amplitudes/intensities doesn't cause any problem. If you run from the GUI, you will have the chance to set the correct columns in AutoBuild, if amplitudes are available in your data file. From the command_line, for existing versions, you would need to say when you run AutoMR: input_labels='F SIGF' (or whatever your amplitudes are in this MTZ file) All the best, Tom T > Hi Tom, > > What about the AutoMR wizard. Can I use intensities there instead of amplitudes? I always get confused. > > Thanks, > > Peter > > 2007/12/18, Tom Terwilliger <terwilliger(a)lanl.gov>: >> Hi phenix.autobuild users, >> I'm sorry to report a serious bug that I have just noticed that applies to MTZ files for autobuild containing intensities. The >> problem is fixed now. I'm very sorry about this mistake. >> All the best, >> -Tom T >> >> >> THE PROBLEM: >> >> In all alpha and beta versions of phenix up to now (up to 1.3b/rc6), there has been a bug in autobuild in which the command >> >> phenix.autobuild data.mtz model.pdb >> >> will misinterpret intensity data as amplitudes if the input file is an mtz file (for example if the mtz file has IMEAN,SIGIMEAN and F,SIGF). (This can also happen in the GUI version, but you will have been presented on screen 3 with a list of data types (FP SIGFP) and columns from the input data file to match them and it is not so likely that you will have chosen to match FP with IMEAN.) >> >> You can tell if this has happened in your case by looking for >> something like (search for the string "Input labels:"): >> >> Input labels: ['IMEAN', 'SIGIMEAN', 'None', 'None', 'None', 'None', 'None', 'None', 'FreeR_flag'] >> >> in your log file (where the None's don't matter, just the first 2 column names. The columns in this list should be >> amplitude-containing columns only. If everything is ok.it should look instead like: >> >> Input labels: ['F', 'SIGF', 'None', 'None', 'None', 'None', 'None', 'None', 'None'] >> >> THE SOLUTION: >> >> In existing versions, the solution to this is to either (1) only have amplitude arrays in your mtz file, or (2) use the GUI and select the correct amplitude arrays, or (3) specify what amplitude columns to use with a command like: >> >> input_labels="F SIGF". >> >> Note that you cannot use intensity data from an mtz file with the existing versions of autobuild, only amplitude data. In the corrected version (1.3b/rc7, not yet out) , you will be able to use an mtz file with intensity data as long as there is no amplitude data in the same mtz file. >> >> Note also that all this applies equally to the refinement_file and hires_file data. Also note that if the file type is not mtz, then this bug does not apply (because the file is always imported and converted from intensities to amplitudes automatically). >> >> >> >> >> >> >> >> >> >> 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 >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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after_autosol
by Bryan W. Lepore 18 Dec '07

18 Dec '07

using phenix 1.3b of 21-10-2007, trying `phenix.autobuild after_autosol` : how does one identify the "highest-numbered AutoSol run", and that it is completed? what does `phenix.autobuild` want for such a solution e.g. in terms of files/directories? or does `phenix.autobuild after_autosol` need to be included in the command at the time when `phenix.autosol` is submitted? phenix.autobuild reads a lot of params from my AutoSol dir, but apparently no solutions -- even though `phenix.autosol show_runs` shows one. -bryan

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chain definition in phenix
by Kornelius Zeth 18 Dec '07

18 Dec '07

Dear all, I'm trying to refine/rebuild a structure of 48 identical chains. In Refmac the small letters a, b, c and 0 1 2 for the chains work quite well and are distinguished. However that does not apply to Phenix which sees A equal to a. What might be the solution to use? Thanks and best wishes Kornelius ---------------------------------------------- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.zeth(a)tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349

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Re: [phenixbb] Resolution Limits in the transition from AutoMR to AutoBuild
by Tom Terwilliger 17 Dec '07

17 Dec '07

Hi Dale, Thanks for the notes! Here is what is supposed to happen: the autobuild wizard keeps all the data you supply. resolution=2.2 will set the resolution of model-building and density modification and refinement refinement_resolution=2.3 will set the resolution for refinement to 2.3 instead of the 2.2 defined by resolution=2.2 There is as you guessed a bug however somewhere in the communication between the autobuild wizard and phenix.refine, so the refinement_resolution did not get passed properly. I will fix that... Thanks! -Tom T . At 01:29 AM 12/17/2007, Dale Tronrud wrote: > The structure factors that I downloaded from the PDB for my >little MR project contains both reflections behind the beam stop >and reflections of higher resolution than even the original authors >would use. When setting up the MR I entered the more restrictive >resolution limits into the Wizard and Phaser appears to have obeyed. > > As near as I can tell from the log files, however, Resolve is >using all the data in the rebuild. I am including a copy of the >log file from the "best" refinement. I would prefer that only >data between 30 and 2.2A were used but it is clear that the >refinement is, at least, monitoring the fit to all the data. I >am presuming that the program is refining against the same data >it is monitoring. > > I would like to suggest that either the log file be clearer >about the resolution limits it is actually refining to, or the >plumbing that passes the resolution limits from the AutoMR wizard >to the AutoBuild wizard be checked. > >Dale Tronrud > >P.S. That's all my problems... For now. The project I'm working >on is cursed and brings out the worst in all the software I have >used. > 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

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A Small Problem with Atom Types in AutoBuild
by Dale Tronrud 17 Dec '07

17 Dec '07

The probe model in my MR project comes from a Shelxl refinement, and the .pdb file does not contain atom types at the end of each ATOM statement as modern .pdb files do. I have magnesium atoms in my model and the atom names for these atoms are "MG" and are properly shifted one space to the left of place where atoms with single letter element symbols lie. Phaser has no problem with this .pdb file. Resolve, however, considers this to be a fatal error. Opening MR.1.pdb and reading coordinates Warning...unknown atom type "M " ...this may indicate characters in columns 77-78 of this PDB file that are not the element ID. This and all similar labels ignored Failed to read line in PDB entry The PDB line is: ATOM 2953 MG BCL B 1 26.429 2.746 -11.155 1.00 12.03 Sorry could not read model file MR.1.pdb Seems a little harsh to me. Especially since the error message doesn't make it back to the log file monitored by the Wizard. I was confused about what was causing the wizard to stop until I dug into the other files in the AutoBuild directory. Earlier in the log file the program worries about my atoms "NA" and "NB" but does conclude that they are nitrogen atoms. In the future I'll work with .pdb files with the extra atom types at the end of the line. Dale Tronrud

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