- phenixbb - phenix-online.org

AutoSol/Heavy atom sites/outside the model
by Egor Tchesnokov 03 Dec '13

03 Dec '13

Thank you for the feedback. WinCoot 0.7/Draw/Cell Symmetry brings up "Show Symmetry" window, which only allows to alter the display but not to coincide the heavy atom sites with the model. Am I not looking at the right menu in Coot ? Thank you for your time and help. Egor

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Autobuild combine
by Heather L Condurso 02 Dec '13

02 Dec '13

Hi all, I am still having issues with Autobuild giving errors during the combine step. I've downloaded the latest build and hope that will solve the problem, but in the mean time I'm having an issue trying to combine the models. I've been following the script: #!/bin/csh -f #COMBINE_MODELS SCRIPT if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1 > dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT # Here are the two log files. I used the expl_fobs_phases_freeR_flags.mtz as fobs.mtz and changed each overall_best.pdb and overall_best_refine_map_coeffs.mtz as the model and map to combine. Thanks, Heather

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AutoSol/Heavy atom sites/outside the model
by Egor Tchesnokov 02 Dec '13

02 Dec '13

Hello, Level: beginner 1. Data collected at wavelength of 0.9537 2. Ran Xtriage: anomalous data seem to extend to 2.2 A 3. Ran Phaser-MR to get partial model (1 copy in AU) 4. Ran AutoSol using partial model and anomalous data AutoSol finds heavy atom sites (FOM=0.69; Overall score=75.6+/-3.3). Coot displays model/density without heavy atoms Heavy atoms are displayed outside the model (using zoom out). Question: what did I do wrong? Thank you for your time and help. Egor

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Red patches of electron density
by Singh, Bishal 01 Dec '13

01 Dec '13

Hi, I am solving a crystal structure at 1.2 Å with completeness 97.3% in the highest resolution shell. There are few small patches of red electron densities on the main chain of a flexible loop at a contour level of ~3sigma of difference ED map. Refinement parameters were following: XYZ coordinates, individual B-factor, optimize X-ray/stereochemistry weight, optimize X-ray/ADP weight and individual Anisotropic ADP for amino acids excluding hydrogen. Target weights are as default in phenix.refine. I already have observed two alternative conformation for this region in another crystal structure. Therefore I am thinking that these red patches are because of lower occupancy of these residues. Please suggest me what shall I do. I shall be grateful for your words. With regards, Bishal Singh University of Heidelberg, Germany

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Iterative build omit map error
by Heather L Condurso 27 Nov '13

27 Nov '13

SO just as my omit map run should have finished, it gave an error instead. I'm running 1.8.4-1496 on a Mac with OSX 10.6.8 and 8GB of memory. Here is the end of the log file: Splitting work into 32 jobs and running with 1 processors using sh background=False in /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_3.log Starting job 4...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_4.log Starting job 5...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_5.log Starting job 6...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_6.log Starting job 7...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_7.log Starting job 8...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_8.log Starting job 9...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_9.log Starting job 10...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_10.log Starting job 11...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_11.log Starting job 12...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_12.log Starting job 13...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_13.log Starting job 14...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_14.log Starting job 15...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_15.log Starting job 16...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_16.log Starting job 17...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_17.log Starting job 18...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_18.log Starting job 19...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_19.log Starting job 20...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_20.log Starting job 21...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_21.log Starting job 22...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_22.log Starting job 23...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_23.log Starting job 24...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_24.log Starting job 25...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_25.log Starting job 26...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_26.log Starting job 27...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_27.log Starting job 28...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_28.log Starting job 29...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_29.log Starting job 30...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_30.log Starting job 31...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_31.log Starting job 32...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Can this be salvaged? It took 5 days to run. I found a section about this in the documentation, but I can't find the maps for each region overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. I can only find working_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. Will these maps work? Can you tell what the error means so that I can avoid this problem in the future? Thanks, Heather

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zero B-factors
by Edna Patricia Matta, Ms 25 Nov '13

25 Nov '13

Hello, Recently I did submit a structure to the PDB but they found that some atoms had zero value for the B-factors. I am new in this filed and I do not know what to do. There have been reports of problems with some versions of phenix about this. I used Phenix 1.8. I repeted the refinement doing restrain NCS-related B-factors but I do not find where to check for the the B-factor values in the the log file. Somebody can help me? Thanks a lot, Edna

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Re: [phenixbb] [ccp4bb] Ligandfit - problem with ligand_start
by Terwilliger, Thomas C 25 Nov '13

25 Nov '13

Hi Danilo, The most likely problem is that the ligand_start file has to have enough atoms in it to define a fixed group in the ligand. The way that ligandfit works is that it breaks a ligand up into rigid groups connected by rotatable bonds. The ligand_start file has to contain one complete rigid group. So probably if you supply a little more of the ligand then it might run. Just to test this, can you try this test of using a ligand_start file: phenix_regression.wizards.test_resolve resolve test_fit_start And then if that gives an "OK", try this: cd test_fit_start phenix.ligandfit ligand=side.pdb ligand_start=start.pdb resolve_map.mtz quick=true Does that run? If you the look at LigandFit_run_1_/TEMP0/resolve_ligand_fit.log Does that say >ligand_start start.pdb Starting configuration of ligand will be read from: start.pdb If all that works, then try adding more atoms to your ligand_start file. Let me know if that doesn't do it! All the best, Tom T Dear all, I am working on a membrane protein covalently bound to a molecular antanna: it is known that this molecule binds to lysine residue but I do not know how many and which lysine residues it binds. 20 diffraction datasets of this protein-ligand complex have been obtained and now, I would quickly localize the ligand using the Fo-Fc map of each data set and using the information on the covalent bound protein-ligand. Ligandfit tool (PHENIX) seems to be indicated to do this; to use the information on the covalent bound, I am using the ligand_start keyword with a pdb containing a ghost atom (however present in ligand model) perfectly superposed to the lysine atom that should bind the ligand. The command used is: phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \ refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif description: - prot.mtz (data) - prot.pdb (protein without ligand) - lig.pdb (ligand containing ghost atom) - lig_start.pdb (ghost atom superpose to NZ of a lysine) - lig.cif (restrain of lig.pdb) Strangely, no ligand is found at the end of the process even reducing ligand_cc_min to 0.01. I have run the same command by using an other protein where an other ligand has been correctly fitted but, also in this case, no ligand has been detected. Conversely, without the use of ligand_start, ligandfit properly localizes the ligand. I'm doing some mistake in the use of ligand_start? Do you know an other tool to perform a ligand fitting in these conditions? Thanks for your answers. Danilo

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Ligandfit - problem with ligand_start
by Danilo Belviso 25 Nov '13

25 Nov '13

Dear all, I am working on a membrane protein bound to a antenna molecule: I know that the molecule binds to lysine residue but I do not know how many and which lysine residues it binds. 20 diffraction datasets of protein-ligand complex have been obtained and now, I would quickly localize the ligand using the Fo-Fc map of each data set and using the information on the covalent bound protein-ligand. Ligandfit tool (PHENIX) seems to be indicated to do this; to use the information on the covalent bound, I have thought to use the ligand_start keyword with a pdb containing a ghost atom (however present in ligand model) perfectly superposed to the lysine atom that should bind the ligand. The command used is: phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \ refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif description: - prot.mtz (data) - prot.pdb (protein without ligand) - lig.pdb (ligand containing ghost atom) - lig_start.pdb (ghost atom superpose to NZ of a lysine) - lig.cif (restrain of lig.pdb) At the end of the processing, ligand is not found. So, I have tryed with ligand_cc_min=0.01, but also in this case ligandfit does not give result. I have thought that no ligand is present. However, to be sure that all was correct, I have run the same command by using an other protein where an other ligand has been correctly fitted. Also in this case, no result has been obtained. Conversely, without the use of ligand_start, ligandfit properly localizes the ligand. I'm doing some mistake in the use of ligand_start? Thanks for your answers. Danilo

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using reference model with polyA chain.
by Francis Reyes 19 Nov '13

19 Nov '13

I'm refining a structure ( at low res ), so I trimmed off all the side chain atoms from my model while my reference model still has these chains. I'm receiving errors like... ----------Correcting rotamer outliers to match reference model---------- ** evaluating rotamers for working model ** A 502 ILE is missing some sidechain atoms, **skipping** A 504 LYS is missing some sidechain atoms, **skipping** A 505 VAL is missing some sidechain atoms, **skipping** I don't care about the side chain atoms, but I'd still like the reference model restraints to provide secondary structure. Does "**skipping**" mean that the reference model is no longer being considered for the particular residue? Or will I still retain my secondary structure from the reference model? Thanks, F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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completeness problem in phenix.refine
by Yarrow Madrona 19 Nov '13

19 Nov '13

Hi, I recently merged two data sets, one having a phase and the other Amplitudes. For some reason my completeness is always 50%. I had anomalous data but the completeness is around 100% after processing and when I do an mtz dump. I'm confused why I get a completeness of 50%. Thank you for any help you can provide. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Error: "Error running main function (INPUT): LLG completion peak selection method not recognized"
by Egor Tchesnokov 18 Nov '13

18 Nov '13

Hello, I am trying to run Phaser/SAD or Phaser/MR_SAD (GUI using defaults), but I get the following error: "Error running main function (INPUT): LLG completion peak selection method not recognized". Thank you for your help Egor

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MSE out density after phenix.refine
by Pavel Afonine 15 Nov '13

15 Nov '13

Hello, anyone experiencing problems related to MSE residues being pushed out density after phenix.refine run should update to next Phenix nightly build, which should fix this problem. Please let me know otherwise off-list. Pavel

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MR_Rosetta prerefine question
by Heather L Condurso 12 Nov '13

12 Nov '13

Dear all, I am trying to use the rosetta prerefinement fuction of MR_rosetta to complete a homology model with missing stretches of amino acids. Everything runs fine and residues are being added to fill the gaps using the fragment files, but rosetta is also altering parts of the model which should already be well placed. Is there a way to tell Rosetta only to prerefine certain residues? I've been following the command line suggestion: phenix.mr_rosetta \ seq_file=seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=100 \ ncs_copies=2 \ space_group=p212121 \ use_all_plausible_sg=False \ nproc=200 \ group_run_command=qsub Thanks, Heather Condurso condurso(a)bc.edu

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Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS
by qwertgfdsa78 11 Nov '13

11 Nov '13

Hi All, I tried Jan's tutorial and finally I was able to install and ran phenix.rosetta with test set 1yjp successfully. However, when I tried my data, I always got *"terminate called after throwing an instance of 'std::bad_alloc'"* Google suggests maybe memory is not enough. I used VirutalBox and assign 8gb memory to it. My protein has ~3000 residues. I guess this will use more memory but how much RAM I need? Or the error is due to some other problem? Thank for any inputs. Lee > ------------------------------ > > Message: 3 > Date: Tue, 05 Nov 2013 14:26:00 +0100 > From: Jan Gebauer <jan.gebauer(a)uni-koeln.de> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS > Message-ID: <5278F1E8.9020602(a)uni-koeln.de> > Content-Type: text/plain; charset="utf-8" > > Hi David, hi all, > > I now managed to at least get a test refinement working. What I mostly > changed was the Ubuntu version. > I have no idea why, but I managed to get it to work on Ubuntu 10.04. > > In principle I installed 10.04 freshly in a virtualbox and from their it > worked rather straight-forward. > > Here is how I proceeded in detail for those of you who are interested: > > 1) Setting up a Virtualbox 4.3.2 r90405 on Ubuntu 12.04.3. > 2) Installing the 64bit version of Ubuntu 10.04 in a virtualbox (4 > processors / 90% speed cap / 4GB Ram /VT-x enabled) > 3) Install VBoxAdditions > 4) Update ubuntu (sudo apt-get update) > 5) Installing g++ and zlib library (sudo apt-get install g++ zlib1g-dev) > 6) Installing binary version of phenix-dev-1525 to > /usr/local/science/phenix-dev-1525 (sudo ./install > --prefix=/usr/local/science) > 7) Unpack rosetta_2013_wk42_bundle to > /usr/local/science/rosetta_2013_wk42_bundle > 8) set rossetta variables by inserting them at the start of > /usr/local/science/pheninx-dev-1525/phenix_env.sh (just in line 3ff): > export PHENIX_ROSETTA_PATH=/usr/local/science/rosetta_2013wk42_bundle > export ROSETTA3_DB=/usr/local/science/rosetta_2013wk42_bundle/main/database > export > PATH=$PATH:/usr/local/science/rosetta_2013wk42_bundle/main/source/bin > 9) assign ownership to active user (sudo chown gebauer:gebauer > /usr/local/science/ -R) > 10) Compile it (phenix.build_phenix_interface nproc=4) > It should run without problems > > Testing: > 1) Create a new directory (mkdir test && cd test) > 2) Download testset (suggested by Nat: phenix.fetch_pdb --mtz 1yjp) > 3) Run rosetta_refine (phenix.rosetta_refine 1yjp.pdb 1yjp.mtz nproc=4) > In my case rFree dropped from 18.21 to 14.90. It's not a low resolution > dataset, but it show that it general works and lowRes would potentially > take to long for a mere testing > > My real data are still being processed so I have no idea how well it > will works... only thing I found out already: > 4.5 GB RAM for 4 processes calculating ~500Aa via rosetta seems not to > be enough. I thereby reduced my "real run" to only one processor... > > Regards, > Jan > > >

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structure factor labels in phenix.refine
by Tanner, John J. 08 Nov '13

08 Nov '13

I have two questions about which structure factor amplitudes are refined against in phenix.refine. 1. Which structure factor amplitude is used in refinement when the labels in the .def file are the following? labels = "F-obs(+),SIGF-obs(+),F-obs(-),SIGF-obs(-)" 2. Is anomalous data used in the refinement when the labels are as follows? labels = "F,SIGF,DANO,SIGDANO,ISYM" I ask these questions because I am wondering which structure factor amplitudes to deposit, and I am trying to rationalize differences between R-factors from refinement and Generate Table 1. Thanks. Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

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few questions about resolving new structure through MR
by Zhihong Yu 07 Nov '13

07 Nov '13

Hi, all I'm a rookie in resolving a brand new structure. I have some questions for my current case and look forward to some suggestions. Now I’m working on a protein like this: N-ter(55aa)—domainA(110aa)—linker(30aa)—domainB(150aa)—C-ter(20aa), I got a diffraction data just to 3.5Å, and there is no complete homology structure in pdb bank, but only a homology structure (named as structureX later) for domainB with ~30% sequence identity, so I have some questions as following: 1. Is it possible to find a resolution through MR approach using structureX as a search model? Especially considering that the resolution is only 3.5Å. Currently I just tried once using phaser and refine the structure for 3 cycyles, I can get a R/Rfree of 0.45/0.55, and it looks like most of backbone in the structureX, especially those within helix or sheet, can be well described by 2Fo-Fc density. Is this primary result promising or not? 2. If it’s possible, what’s the general optimal procedure I should follow? Really thanks for any advice and suggestions! Zhihong

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Issue with SeMet residues
by Mark Wilson 07 Nov '13

07 Nov '13

Dear PHENIX users and developers, I am refining a structure containing SeMet residues at atomic (1.05 Å) resolution. The model was initially refined in Refmac5 and behaved as expected (i.e. reasonable R factors and agreement with maps). I've used this final Refmac5 model as a starting point for refinement in PHENIX 1.8.4 with standard settings, as below. phenix.refine data.mtz \ refinement.input.xray_data.labels="F, SIGF" model.pdb \ main.use_experimental_phases=false \ refinement.main.number_of_macro_cycles=5 output.prefix="model_refine"> phenix_refine_1.log Strangely, the conformations of the MSE residues are changed quite significantly after refinement in PHENIX, departing both from electron density and from the prior model. Any help would be appreciated. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilson13(a)unl.edu

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Issues using reference model with Autobuild
by Dan McNamara 07 Nov '13

07 Nov '13

Hello all, I'm hoping to troubleshoot a problem with autobuild and the use of a reference model. Autobuild has been always failing once it gets to the initial refinement step and attempts to add reference model restraints. I've included my autobuild parameterization. Refinement is where it dies and the contents of LAST.LOG and my error log file are below too. I'm not sure how to get the reference model file location properly interpreted. I even tried manually moving the reference PDB into the AutoBuild_run_X_/ and TEMP0/ folders as they're generated to no avail. Best, Dan phenix.autobuild \ data=/home/.../xyz.mtz \ refinement_file=/home/.../xyz.mtz \ input_refinement_labels="FP SIGFP FreeRflag" \ model=/home/.../xyz.pdb \ seq_file=/home/.../xyz.dat \ s_annealing=False \ rebuild_in_place=True \ n_cycle_rebuild_max=3 \ refine_eff_file=/home/.../xyz.eff \ refine_with_ncs=True \ model_building.reference_model=/home/.../def.pdb \ #I have also tried locations like ../def.pdb and def.pdb that give Errno 21 or Errno 2 below nproc=200 \ general.run_command="/home/.../xyz.sh" AutoBuild_run_1_/LAST.LOG: ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (30132 atoms) torsion_angles = False (0 atoms) rigid_body = True (30120 atoms in 24 groups) individual_adp = False (iso = 0 aniso = 0) group_adp = True (30132 atoms in 4092 groups) tls = True (30120 atoms in 147 groups) occupancies = True (12 atoms) group_anomalous = False n_use = 30132 n_use_u_both = 30120 n_use_u_iso = 12 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 30132 *** Adding Reference Model Restraints *** errors.txt: Sorry: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_1_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/.../AutoBuild_run_1_/LAST.LOG may have additional information... Cannot open file for reading: "/" [Errno 21] Is a directory: '/' ******************************************************************************** Sorry: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/.../AutoBuild_run_2_/LAST.LOG may have additional information... Cannot open file for reading: "." [Errno 21] Is a directory: '.' ******************************************************************************** Sorry: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_3_/TEMP0/NO_LIG_NO_WAT_xyz_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/.../AutoBuild_run_3_/LAST.LOG may have additional information... Cannot open file for reading: "d" [Errno 2] No such file or directory: 'd' ********************************************************************************

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Sigmas of F+ and F- equal in _data file
by Tanner, John J. 07 Nov '13

07 Nov '13

I have a question about the _data.mtz file that phenix.refine outputs (version 1.8-1069). It appears that sigmaF+ equals sigmaF- for each reflection in the _data.mtz file, although they were unequal in the input .mtz file. You can compare the input mtz and the output _data.mtz file by viewing these links: http://faculty.missouri.edu/~tannerjj/input.jpeg http://faculty.missouri.edu/~tannerjj/samesigma.jpeg Thanks. Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

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real-space refinement
by "Weiergräber, Oliver H." 06 Nov '13

06 Nov '13

Hello, beginning with phenix 1.8.3, the individual_sites_real_space option will not run globally if, e.g., R < 0.25. Is there a way to force the original behaviour? Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Is the protein-ligand complex structure model right??
by Wei Shi 06 Nov '13

06 Nov '13

Hi all, I am trying to solve a protein-ligand complex structure. The resolution of the data is 2.8Å. The molecular replacement solution is found in space group P21 21 21. The current best model: start final ------------------------------------------------ R-work: 0.2836 0.2484 R-free: 0.3236 0.3066 RMS(angles): 0.60 0.63 RMS(bonds): 0.002 0.002 ==============MolProbity validation ============== Ramachandran outliers: 2.4% (Goal: < 0.2%) Ramachandran favored: 89.2% (Goal: > 98%) Rotamer outliers: 4.7% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 10.89 Overall score: 2.64 Four ligands are placed for every dimer of the protein. And we are not sure whether we put the ligands right, since first it's thought that only two ligands bind every dimer of the protein. I created a SA omit map (composite). The density for the most of the N-terminal DNA binding domain is very bad, and the density for C-terminal ligand binding domain is much better. And, I could see density for all 4 ligands. Does this necessarily mean that the model for the N-terminal DNA binding domain is not right or should I try other types of omit map (simple, refined or iterative building)? Also, I am wondering what's the difference between different types of omit map (simple, refined, iterative building) and whether it's the most reliable method to tell whether the structure model is right. So, I am not sure whether the structure model I have is correct. It's suspected that the molecular solution is in the wrong space group or the data is twinned and only two ligands bind every dimer of the protein......But, I am not sure what I should check or what to do to improve the model. Thank you so much! Best, Wei

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Is the protein-ligand complex structure model right??
by Wei Shi 05 Nov '13

05 Nov '13

Hi all, I am trying to solve a protein-ligand complex structure. The resolution of the data is 2.8Å. The molecular replacement solution is found in space group P21 21 21. The current best model: start final ------------------------------------------------ R-work: 0.2836 0.2484 R-free: 0.3236 0.3066 RMS(angles): 0.60 0.63 RMS(bonds): 0.002 0.002 ==============MolProbity validation ============== Ramachandran outliers: 2.4% (Goal: < 0.2%) Ramachandran favored: 89.2% (Goal: > 98%) Rotamer outliers: 4.7% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 10.89 Overall score: 2.64 Four ligands are placed for every dimer of the protein. And we are not sure whether we put the ligands right, since first it's thought that only two ligands bind every dimer of the protein. I created a SA omit map (composite). The density for the most of the N-terminal DNA binding domain is very bad, and the density for C-terminal ligand binding domain is much better. And, I could see density for all 4 ligands. Does this necessarily mean that the model for the N-terminal DNA binding domain is not right or should I try other types of omit map (simple, refined or iterative building)? Also, I am wondering what's the difference between different types of omit map (simple, refined, iterative building) and whether it's the most reliable method to tell whether the structure model is right. So, I am not sure whether the structure model I have is correct. It's suspected that the molecular solution is in the wrong space group or the data is twinned and only two ligands bind every dimer of the protein......But, I am not sure what I should check or what to do to improve the model. Thank you so much! Best, Wei

1 0

Green density for ligands in places where the ligand is in density
by Wei Shi 05 Nov '13

05 Nov '13

Hi guys, I am working with a protein-ligand complex structure. I generated the ligand pdb and cif with Phenix.eLBOW. Then, I fit the ligand to density (green or continuous blue denisty) in Coot. Then, I did a refinement of the protein-ligand complex model in Phenix. I opened the refinement results in Coot, I don't know why in some places where the ligand is in density, it always shows green density in Coot... And, from the pdb file, the occupancy for all ligands are 0? Do any of you happens to know whether this is unusual and what might go wrong? Thank you so much! Best, Wei

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Re: [phenixbb] Restraints generation for TaBr
by Rebecca Oot 05 Nov '13

05 Nov '13

Hi Nigel, Thanks so much for the response, the information and for the files. Best, Rebecca

1 0

Re: [phenixbb] Restraints generation for TaBr
by Rebecca Oot 05 Nov '13

05 Nov '13

Hi Anshul, Thanks very much for the files--much appreciated!! Hope all is well. Rebecca

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