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weird B factor refinement
by Sebastiano Pasqualato 24 Mar '11

24 Mar '11

Hi all, I am refining a structure and have turned on TLS refinement. Since I have done this, I see a weird behavior in some sulphur atom's B factor, and their near atoms. I paste below an example. Has anybody else seen this? Looks like a bug... Thanks a lot in advance, ciao, s ATOM 655 N PHE A 82 66.343 -40.145 -6.536 1.00 25.85 N ANISOU 655 N PHE A 82 3247 3386 3190 162 103 157 N ATOM 656 CA PHE A 82 65.631 -38.890 -6.206 1.00 23.86 C ANISOU 656 CA PHE A 82 2967 3126 2971 192 102 153 C ATOM 657 C PHE A 82 64.134 -39.032 -6.460 1.00 27.82 C ANISOU 657 C PHE A 82 3494 3640 3436 176 116 173 C ATOM 658 O PHE A 82 63.709 -39.388 -7.568 1.00 46.67 O ANISOU 658 O PHE A 82 5852 6065 5815 251 147 222 O ATOM 659 CB PHE A 82 66.174 -37.668 -6.970 1.00 14.67 C ANISOU 659 CB PHE A 82 1831 1971 1772 176 119 175 C ATOM 660 CG PHE A 82 65.501 -36.397 -6.574 1.00 25.83 C ANISOU 660 CG PHE A 82 3217 3375 3223 210 117 169 C ATOM 661 CD1 PHE A 82 64.399 -35.932 -7.285 1.00 19.12 C ANISOU 661 CD1 PHE A 82 2363 2528 2371 221 125 179 C ATOM 662 CD2 PHE A 82 65.919 -35.707 -5.429 1.00 37.72 C ANISOU 662 CD2 PHE A 82 4725 4876 4732 206 117 168 C ATOM 663 CE1 PHE A 82 63.734 -34.784 -6.874 1.00 23.74 C ANISOU 663 CE1 PHE A 82 2979 3122 2919 200 145 205 C ATOM 664 CE2 PHE A 82 65.275 -34.544 -5.018 1.00 34.01 C ANISOU 664 CE2 PHE A 82 4257 4438 4226 262 171 240 C ATOM 665 CZ PHE A 82 64.176 -34.080 -5.744 1.00 33.79 C ANISOU 665 CZ PHE A 82 4254 4389 4196 197 145 203 C ATOM 666 N CYS A 83 63.337 -38.791 -5.425 1.00 35.53 N ANISOU 666 N CYS A 83 4471 4615 4413 176 117 175 N ATOM 667 CA CYS A 83 61.879 -38.960 -5.524 1.00 55.90 C ANISOU 667 CA CYS A 83 7050 7200 6991 181 121 181 C ATOM 668 C CYS A 83 61.332 -37.537 -5.259 1.00 48.88 C ANISOU 668 C CYS A 83 6132 6340 6100 265 163 240 C ATOM 669 O CYS A 83 61.949 -36.777 -4.512 1.00 50.54 O ANISOU 669 O CYS A 83 6344 6544 6313 262 165 239 O ATOM 670 CB CYS A 83 61.343 -40.122 -4.596 1.00 2.87 C ANISOU 670 CB CYS A 83 332 481 275 174 114 172 C ATOM 671 SG CYS A 83 61.739 -41.776 -5.153 1.00212.79 S ANISOU 671 SG CYS A 83 26919 27069 26861 166 105 162 S ATOM 672 N ASP A 84 60.251 -37.131 -5.925 1.00 46.73 N ANISOU 672 N ASP A 84 5887 6042 5827 199 138 202 N ATOM 673 CA ASP A 84 59.894 -35.684 -6.003 1.00 53.97 C ANISOU 673 CA ASP A 84 6774 6990 6743 291 187 268 C ATOM 674 C ASP A 84 59.468 -34.966 -4.713 1.00 54.16 C ANISOU 674 C ASP A 84 6797 6968 6812 239 140 198 C ATOM 675 O ASP A 84 59.898 -33.835 -4.448 1.00 54.40 O ANISOU 675 O ASP A 84 6861 7005 6804 211 158 221 O ATOM 676 CB ASP A 84 58.829 -35.479 -7.062 1.00 52.17 C ANISOU 676 CB ASP A 84 6574 6736 6511 218 157 225 C ATOM 677 CG ASP A 84 59.320 -35.845 -8.416 1.00 59.41 C ANISOU 677 CG ASP A 84 7456 7647 7469 252 143 207 C ATOM 678 OD1 ASP A 84 60.375 -35.284 -8.783 1.00 61.87 O ANISOU 678 OD1 ASP A 84 7770 7956 7782 252 144 207 O ATOM 679 OD2 ASP A 84 58.683 -36.697 -9.087 1.00 57.64 O ANISOU 679 OD2 ASP A 84 7230 7428 7243 253 141 207 O -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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B factor statistics
by Yuri 24 Mar '11

24 Mar '11

Hello phenixers, I am putting together a crystallography table for my model, what is the best way to find the average B factors. Are they broken down by main chain, side chain and HOH? thank you -- Yuri Pompeu

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reference model
by Kendall Nettles 24 Mar '11

24 Mar '11

Dear PHENIX developers, I would like to use a reference model in refinement, but the structure has two components with known higher resolution structures. Can I specify two reference models? How? I'm also having trouble with the syntax. With the following params file, the run fails saying that reference model is an unused parameter. Lastly, what does "reference_xray_structure" do? Thanks! Kendall refinement.main { reference_model_restraints = True } refinement.refine { strategy = *individual_sites \ rigid_body \ individual_sites_real_space \ *individual_adp \ group_adp \ tls \ occupancies \ group_anomalous \ none } reference_model { file = 4.pdb }

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Re: [phenixbb] rotamers
by Phoebe Rice 24 Mar '11

24 Mar '11

I'm moderately in favor of the "just let B go through the roof" option. Here's why: Most "user friendly" programs like pymol have an option to color the atoms by B but not by occupancy. Most end-users I interact with know enough to see if coloring by B makes a side chain flaming red, but they'd never think (or know how) to check occupancy. (So if you do set occ to zero, please set B to the max!) And truncating side chains screws up simple electrostatics calculations, which matters if you deal with nucleic acid-binding proteins. Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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pdb editor after autobuild
by Jason 23 Mar '11

23 Mar '11

Hi, I have a pdb file obtained from autobuild. However, some of the sidechains are missing. Is there an easy way to detect which sidechains are missing? The reason I am asking is my pdb file is huge. It takes a lot of effort to go through one reside by one residue. Thanks. -- ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Low rmsd values
by Teemu Haikarainen 23 Mar '11

23 Mar '11

Hi all, I am getting quite low rmsd values for my structure. I am finishing the refinement and I have rmsd of 0.003 Å for bonds and 0.67 for angles, with R/Rfree of 0.148/0.176. The resolution is 2.0 Å. I am refining with riding hydrogens and using the automatic weight optimization. I have also tried to change the weights manually, but the more eye-pleasing rmsd values always result in worse Rfree. Is there any reason to worry about the low rmsd values and should I always use the optimized weights in refinement? I am using the latest version of Phenix. Regards, Teemu -- Teemu Haikarainen (M.Sc.) Turku Centre for Biotechnology Tykistokatu 6 BioCity, Turku FIN-20521, Finland

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Re: [phenixbb] Autobuild parent process aborted--running combine_models in Autobuild
by Thomas C. Terwilliger 22 Mar '11

22 Mar '11

Hi Mark, The answer depends on whether this is a "rebuild_in_place=True" run or not. (I think you are using rebuild_in_place=true, but I'll give both answers): Assuming "rebuild_in_place=True": You can combine models with autobuild, providing all models have exactly the same set of atoms (aside from any solvent) by editing this script (basically you run a dummy autobuild run to create a directory and database entries, then you copy your files there, then you run autobuild and tell it to carry on and do the combine step): #!/bin/csh -f 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 Assuming "rebuild_in_place=False": In this case you can provide autobuild with a list of files with consider_main_chain_list="file1.pdb file2.pdb" , or simply dump all the models into a singe pdb file and use model=all_models.pdb, and run autobuild one more time. Let me know if that doesn't do it! -Tom On Mar 22, 2011, at 3:00 PM, Mark A Saper wrote: I ran AutoBuild from command line and it submitted 5 jobs with qsub. Apparently I aborted the parent process. So I have the 5 jobs running, apparently producing 5 different models (I specified nproc = 5 as suggested in the documentation). Can I rerun AutoBuild and have it combine the 5 models already calculated? Mark _________________________________ Mark A. Saper, Ph.D. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://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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Autobuild parent process aborted
by Mark A Saper 22 Mar '11

22 Mar '11

I ran AutoBuild from command line and it submitted 5 jobs with qsub. Apparently I aborted the parent process. So I have the 5 jobs running, apparently producing 5 different models (I specified nproc = 5 as suggested in the documentation). Can I rerun AutoBuild and have it combine the 5 models already calculated? Mark _________________________________ Mark A. Saper, Ph.D. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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Another question about twinned maps
by Mary Ho 22 Mar '11

22 Mar '11

Pavel- Another related question... Does the option for Fill Missing F(Obs) with F(Calc) work for twinned maps? If I turn it on, I don't get an error but the maps don't seem any different. Just wondering, Thanks, Mary On Mon, Mar 21, 2011 at 11:44 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Mary, > > I'm not sure map sharpening is done in case of twinning (otherwise it is an > option that you can turn on/off either in phenix.refine or in more specific > tool for maps calculation called phenix.maps). I will check this later today > and reply. > > Pavel. > > > > On 3/21/11 8:08 AM, Mary Ho wrote: > >> I'm using phenix-1.7-650. When phenix.refine generates the detwinned maps >> with apply B-factor sharpening on and no value inputed, is the value the >> program uses for sharpening output anywhere? >> >> Thanks, >> >> Mary X. Ho >> Postdoctoral Associate >> Arnold Lab >> Rutgers >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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refinement for ligands with alternative conformation
by zhengyi＠msu.edu 21 Mar '11

21 Mar '11

Hello, I am working on the refinement of a structure about 2.8A, which the substrate ligand has an odd conformation. A blob of negative difference density about 4.8 sigma between the one portion of the ligand and the other. If I break down the ligand into two parts, the negative density disappears, however, one part of the ligands does not fit well. We suspect a mixture of conformations. Any suggestions would be appreciated on how to setup refinement for ligands with alternative conformation. Many thanks, Yi Zheng Department of Biochemistry Michigan State University

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