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Continue from an AutoBuild job abruptly killed
by Miguel Ortiz-Lombardía 17 Jan '08

17 Jan '08

Dear all, We had a problem with a machine running AutoBuild, which resulting in the computer going down and the AutoBuild job consequently killed. I've tried to find out if there is a way to continue the job (it had been running for four days and still had a few hours to go I guess: a pretty big unit cell) but I failed. I would appreciate if someone could point to the relevant pages in the manual/tutorials or give me advice about how to do such a thing. If that's possible, of course. We're using the latest phenix (1.3b-rc6) and cci apps. Thank you! Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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MSE gap
by Troy E Messick 16 Jan '08

16 Jan '08

Hello, I seem to be having a problem with phenix.refine and the seleno-methionine residue (resname MSE). It seems that I have a gap in the peptide bond between the C atoms and the N atom of the subsequent residue. Is there something I could add to the restraints_edits.params file to get it to click together? What is the distance_ideal and sigma for a peptide bond? Thanks for your help, Troy

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phenix.find_ncs and DANO
by Bryan W. Lepore 16 Jan '08

16 Jan '08

in principle, phenix.find_ncs should be fine with FP=DANO, right? and - do i understand correctly that phenix only correlates the map with the .pdb sites, and does not rotate the map about itself (like in getax, i think)? -bryan p.s: i can run phenix.find_ncs with FP=DANO, but seems that resolve wants it to be FP as usual.

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autosol : input_ncs_file
by Bryan W. Lepore 16 Jan '08

16 Jan '08

using PHENIX VERSION: 1.3b of 20-11-2007. does phenix.autosol use "input_ncs_file"? the documentation implies that phenix.autosol will take `input_ncs_file` (at the 'find_ncs' entry, "input_ncs_file" is mentioned but no where else), yet, i get a 'Sorry, unknown file or keyword:' message with no such command line option listed. -bryan

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strategy of refinement for a structure phased by bromide soaking
by Pascal EGEA 11 Jan '08

11 Jan '08

Dear All, I have a 1.8A resolution data set of a protein collected on a crystal soaked in KBr and I am solving using Phenix. I used AutoSol and gave a rough estimate of f_prime and f_double_prime for the Br scatterer as a starting point. It worked great and Phenix found 31 Bromide ions (only one is fully occupied) and the resulting map is remarkably clear. Automatic building has done a great job and I was able to build most of the 4 monomers present in the AU. However I am confused and have a couple of questions. 1-As Phenix started it generated a fobs_experimental_phases_free_Rflag.mtz file. I have been using this file and no longer my data.hkl file for further refinement. I would like to know why the best_solution after the automatic building run does not contain any of the Bromide ions. It has water molecules but no Bromide ions? What is the reason for that? 2-I have been refining against the mtz file I mentioned but without any of these Bromide ions and although the refinement is converging , I suspect I have been doing something bad and wrong. Should I start my refinement again from the first best pdb after automatic building and include right away the bromide ions with simultaneous f_prime, f_double_prime and occupancy refinement for the anomalous scatterers? As it stands now the Rfree is 22.9 and the Rfac is 19.7. The map looks fine except for the solvent, some of this atoms are obviously bromide and there is extra density in the Fo-Fc around some "solvent" atoms. Thanks a lot in advance for your suggestions. Pascal Egea University of California San Francisco Department of Biochemistry and Biophysics

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iotbx.shelx.from_ins
by Foelker, Andrew 10 Jan '08

10 Jan '08

Hello Perhaps one of you could assist me with this question. In the from_ins.py file, there is a function by the name of from_ins. I am passing a .RES file to this function, but am not passing any of the other optional arguments to it. When line 51 in the file is reached, an exception is thrown. Here is the line of code that blows up: b = record.tempFactor + record_next.tempFactor The exception correctly states that the record_next object has no attribute named 'tempFactor'. Perhaps I am doing something incorrectly, or perhaps there is a bug in the from_ins function itself. If any of you can offer some insight into this problem I would greatly appreciate it. Thank you. ------------------------------------------------------------------------ -------- Andrew J. Foelker Software Engineer Bruker AXS Inc. 5465 E. Cheryl Parkway Madison, WI 53711 Tel: +1 608-276-3812 andrew.foelker(a)bruker-axs.com www.bruker-axs.com <http://www.bruker-axs.com/> ------------------------------------------------------------------------ ----------

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Reading Rfree Flags from Refmac
by James Fraser 09 Jan '08

09 Jan '08

Hello, Someone in our lab has started a refinement run in REFMAC and wants to continue it in Phenix.refine. Is there an easy way to get phenix to recognize the r-free flag from REFMAC (freeR=0)? Thanks, jf -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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Failure when calculating a composite omit map
by Dale Tronrud 07 Jan '08

07 Jan '08

Hi all, I'm trying to calculate a composite omit map so that I can get a clear view of a troublesome region in my structure. I have two copies of everything in the asu so I created some dummy atoms to mask the region in the A chain and called those atoms chain Y and another collection to mask the region in the C chain and created a Z chain for them. I put these atoms in a file name Mask.pdb I attempted to calculate the composite omit map starting from my MR solution but that fails because Autobuild doesn't like being given the Fourier coefficients produced by Phaser. To work around this problem I decided to ask it to create the omit map based on the results of my AutoBuild followed the MR. My script is: phenix.autobuild model=AutoBuild_run_12_/overall_best.pdb data=1M50-2.mtz \ input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \ 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 \ composite_omit_type=iterative_build_omit omit_region_specification=omit_around_pdb omit_box_pdb=Mask.pdb\ omit_res_start_list="1 1" omit_res_end_list="39 30" omit_chain_list="Y Z" \ rebuild_in_place=Yes Mask.pdb is attached. Resolve is unable to create a mask. The log file, omit_box_id.log is also attached. Resolve creates a temp file named TMP.pdb which I would expect to contain the contents of my Mask.pdb. It only contains the first set of dummy atoms; chain Y. Then when Resolve reads this file it appears not to find even those atoms. I know Tom is out of reach for quite a while. Is there someone else who could help me over this hurdle? Dale Tronrud

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Autosol Feedback and questions
by Partha Chakrabarti 04 Jan '08

04 Jan '08

Happy new year everybody, I had quite a bit of difficulty with a SAD dataset which also showed Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to refine, AddSOLVE to find more , and both SOLVE and PHASER to solve but it did not get to a point where I could do manual building. Autosol worked beautifully, the input files were scalepack merged data, ha.pdb (from addsolve step), and the sequence. PHASER to solve and TEXTAL & RESOLVE with through build option. This actually leave me with some confusions / questions: 1. When I compare the other "solutions", they look like the right one, just not good enough. Where exactly is the autosol making a difference? Is it the ability of of TEXTAL to build something more meaningful when the solution is not good or number of iterations? 2. How does PHASER know the different anomalous atoms? Does is use a different scaling factor for SE and S? 3. I see that phenix.refine has been used in the internal runs, I have used phenix.refine earlier. But after playing with the side chains in Coot, when I tried to use the modified pdb file and resolve.mtz, it complained about the good old Free_R flag. However, it ran directly in Refmac. Is it a known problem or maybe I did something stupid? I could do a dry run and change the read mtz and not cns if that would solve the problem. 4. Lastly, is it possible to use multiple processors to run the job? Best regards, 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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Re: [phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine
by Thomas C. Terwilliger 03 Jan '08

03 Jan '08

Hi Dale, Can you try something else: phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=\ AutoBuild_run_12/exptl_fobs_freeR_flags.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif This differs from your run only by substituting AutoBuild_run_12/exptl_fobs_freeR_flags.mtz for your 2 refinement data files. This is the exact file that is used in refinement by AutoBuild. I agree that you should be able to use your original data file instead. A possible reason why this has failed is that the original data file has a couple reflections for which there is no data...and which were tossed by AutoBuild before creating exptl_fobs_freeR_flags.mtz . Two files that differ only in reflections with no data will still give different checksums, I think. All the best, Tom T > Hi Dale, > >>> 1) Why you specify reflection MTZ file twice in phenix.refine script? >>> >>> >> I put the mtz in twice because if I put it in once phenix.refine >> complains that I have no free R flags. It seems to want one file with >> the amplitudes and another with the flags. Since I have both in the >> same file I put that file on the line twice and phenix.refine finds >> everything it needs. >> > > phenix.refine looks for free-R flags in your main data file > (1M50-2.mtz). Optionally you can provide a separate file containing > free-R flags (I have to write about this in the manual). However, if > your 1M50-2.mtz contains free-R flags then you don't need to give it > twice. So clearly something is wrong at this step and we need to find > out what is wrong before doing anything else. Could you send the result > of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your > data file? Or I can debug it myself if you send me the data and model. > >> If the MD5 hash of the test set depends on the resolution then >> certainly >> I could be in trouble. > > No. It must always use the original files before any processing. > >> Does the resolution limit affect the MD5 hash of the test set? >> > > No. If it does then it is a very bad bug. I will play with this myself > later tonight. > >> >>> 3) Does this work: >>> >>> (...) >> >> I'll try these but it will take a bit of time. >> > > Don't run it until completion. Just make sure it passed through the > processing step. > > Pavel. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Using the Same Test Set in AutoBuild and Phenix.Refine
by Dale Tronrud 03 Jan '08

03 Jan '08

Hi all, I have another problem, I'm afraid. I have built a model using phenix.autobuild and now want to run some refinement. While in the long run I'll do some manually rebuilding using Coot I just wanted to run a test of phenix.refine to ensure I have the script right and have a baseline to compare against later. My autobuild script is: phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \ 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 My refine script is phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=1M50-2.mtz 1M50-2.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif As you can guess, my test set flags are in the same mtz file as the amplitudes. I'm feeding exactly the same file into both runs. Despite this I get in my output ******************************************************************************* ******************************************************************************* The MD5 checksum for the R-free flags array summarized above is: 785fd03f6881898dcd91bc5f8c3e5b26 The corresponding MD5 checksum in the PDB file summarized above is: 6f86ee71dbcd2dc1f5282cf18547c79b These checksums should be identical but are in fact different. This is because the R-free flags used at previous stages of refinement are different from the R-free flags summarized above. As a consequence, the values for R-free will be biased and misleading. It is best to avoid this situation by consistently using the same R-free flags throughout the refinement of a model. If the previously used R-free flags are still available run this command again with the name of the file containing the original flags as an additional input. If the original R-free flags are unrecoverable, remove the REMARK r_free_flags.md5.hexdigest 6f86ee71dbcd2dc1f5282cf18547c79b record from the input PDB file to proceed with the refinement. In this case the values for R-free will become meaningful only after many cycles of refinement. ******************************************************************************* ******************************************************************************* Sorry: Please resolve the R-free flags mismatch. While I'm glad that Phenix is checking to ensure that I haven't goofed and tried to switch test sets, I believe I'm being unjustly accused. Why does phenix.refine think I'm a bad boy? Dale Tronrud

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Re: [phenixbb] Autosol Feedback and questions
by Ralf W. Grosse-Kunstleve 02 Jan '08

02 Jan '08

Hi Partha, > 3. I see that phenix.refine has been used in the internal runs, I have used > phenix.refine earlier. But after playing with the side chains in Coot, when > I tried to use the modified pdb file and resolve.mtz, it complained about > the good old Free_R flag. Is this the MD5 error message? > However, it ran directly in Refmac. Is it a known > problem or maybe I did something stupid? I could do a dry run and change > the read mtz and not cns if that would solve the problem. I'm not sure what's going wrong. To be sure, I'd need a reproducer, or at least an exact description of what happened in which order. > 4. Lastly, is it possible to use multiple processors to run the job? No, sorry. Parallelization is a big, complex project. The Cambridge group has started some work in this direction, but it is still very experimental. Ralf

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Fatal Error: Incomplete libtbx environment!
by Yong-Fu Li 01 Jan '08

01 Jan '08

Hi, I just installed Phenix 1.3b, however got this error message when I tried to run phenix. ******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command. My system is: 2.6.23.8-34.fc7 i686 Here is what I did: 1) downloaded phenix-installer-1.3b-rc6-intel-linux-2.6.tar 2) tar -xvf ... 3) In directory: phenix-installer-1.3b/, execute ./install 4) moved phenix-1.3b-rc6/ from /usr/local to /usr/local/progs where all of my programs dwell 5) source phenix_env in: /usr/local/progs/Phenix/phenix-1.3b-rc6 6) then run: ./phenix, and got the above message 7) as root go to /libtbx, chmod +x configure.py, and ./configure.py (I don't know about python, and my Python is 2.5), it hangs there for very long (>10 min) with another error: ./configure.py: line 3: syntax error near unexpected token `(' ./configure.py: line 3: `def run():' I checked the bb for help but didn't find any useful info (not finished reading all the messages). I wonder whether someone could help! Thanks and happy new year! Yongfu

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heavy atom sites in autobuild
by Bryan W. Lepore 29 Dec '07

29 Dec '07

i'm confused about treatment of heavy atom sites in autobuild. couple questions : 1. since heavy atom sites can be treated as single atoms, should phenix.autobuild simply refine the positions within a protein model? i.e. heavy atom sites should not need to be treated as ligands, with a .cif -- right? 2. if i want autobuild to build around the heavy atom site, can i just use input_pdb_file=heavy.pdb? input_lig_file_list= is not working. -bryan

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Se SAD data to include Sulphurs?
by Partha Chakrabarti 28 Dec '07

28 Dec '07

Hiya, I have a SAD dataset collected at 0.979A to very good completeness and redundancy, upto 2.1A. Two molecules in AU, each containing 2 Se and the solvent content is 40%. The Signal to noise is more than 1 upto 2.1A , however solve resolve and phaser did not work. I am not an expert but what is getting somewhere is if I use SHELEX (or hyss) to find the sites, pick the best 3 of them, use MLPHARE or so to refine and Addsolve to find the other Se. However, looks like the fourth Se is less ordered. Now, the SHELEX file also finds several others which I guess are Sulphurs. I can see helix like density in the map after Addsolve (& resolve) or SHELEXE but have not been able to place any aromatic residue yet. I guess one problem is lack of proper NCS and low solvent content. Could someone point me to a method in which I can improve the map by including the Sulphurs? For example, using the already found Se as seeds? I am trying the autosol option anyway. Cheers, Partha

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Re: [phenixbb] How do I gather the pieces after AutoBuild?
by Thomas C. Terwilliger 27 Dec '07

27 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 19 Dec '07

19 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 19 Dec '07

19 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 19 Dec '07

19 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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