- phenixbb - phenix-online.org

secondary structure restraints
by Bradley Hintze 28 Mar '11

28 Mar '11

Hello PHENIX developers. When I run phenix.secondary_structure_restraints 1ZY7.pdb format=refmac I get this error: Traceback (most recent call last): File "/Users/bradleyhintze/phenix/phenix-dev-699/cctbx_project/mmtbx/command_line/secondary_structure_restraints.py", line 6, in <module> secondary_structure.run(sys.argv[1:]) File "/Users/bradleyhintze/phenix/phenix-dev-699/cctbx_project/mmtbx/secondary_structure/__init__.py", line 766, in run if (len(proxies) == 0) : NameError: global name 'proxies' is not defined Am I missing something? Also, is there anything like '-h' on phenix.secondary_structure_restraints so that I can figure out the different options? Thanks, Bradley

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differences between command line and GUI?
by Kendall Nettles 28 Mar '11

28 Mar '11

Dear PHENIX developers, I ran a job through the GUI, and then what I thought was the same job on our cluster. The job from the cluster has Rfree that is 0.7% higher. I'm totally at a loss to figure out what is causing this. It is the same version of PHENIX (1.7-650). I then took the .eff file from the GUI job and used that as the params file for the command line job but still get the big difference in R free. Any suggestions? Best regards, Kendall Nettles

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r_free_flags.export_for_ccp4 option of iotbx.reflection_file_editor
by Keitaro Yamashita 26 Mar '11

26 Mar '11

Dear PHENIX developers, I'm using phenix-1.7-650 (current latest). I noticed that r_free_flags.export_for_ccp4 option of iotbx.reflection_file_editor, which convert flag convention to ccp4 style, does always assign 1..19 to working set at random. In CCP4 style, I think working set flag numbers should be 1 .. (1 / fraction - 1). Otherwise, I'm afraid it might have a bad influence on further processing e.g. flag value completion using ccp4 program. I look forward to your response, Keitaro

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modified nucleotide not linked
by tuske＠cabm.rutgers.edu 25 Mar '11

25 Mar '11

Hello all, I am refining three protein-DNA complexes each with a different modified nucleotide-monophosphate residue at the 3'-terminus of its DNA strand. Two of these worked fine after sending the pdb file through ready-set. With the third structure the modified nucleoside-monophosphate residue is not recognized as linked to the previous nucleotide-monophospahe--no phosphodiester bond formation. The only difference between the two that "worked" and the one that didn't is the nature of the deoxyribose sugar modification. The first two have substituents at the 4'-carbon of the deoxyribose sugar, the third has the 4'-oxygen of the deoxyribose sugar substituted with a -CH2- making it a cylcopentyl pseudo-sugar. The bond lengths and angles are reasonable in the starting model, I had no problem doing the initial refinement in CNS after defining topology and parameter files. The output for this in the log file is: Chain: "P" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Unusual residues: {'CAR': 1} Classifications: {'undetermined': 1, 'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {None: 1, 'rna3p': 19} Not linked: pdbres="CYT P 821 " segid="P " pdbres="CAR P 822 " segid="P " Thanks, Steve

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free R test or work set flag value
by Bryan Lepore 25 Mar '11

25 Mar '11

[ dev-705 ] i see: Test (R-free flags) flag value: 1 is the work set the negation? -Bryan

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Postdoctoral position in Grenoble, France - Living deep
by Eric Girard 25 Mar '11

25 Mar '11

*Living deep: Structural basis of piezophilic adaptation* ELMA group. Institut de Biologie Structurale J.-P. Ebel -- Grenoble -- France http://www.ibs.fr/groupes/groupe-extremophiles-et-grands/ We are recruiting a post-doctoral scientist interested in life adaptation to extreme conditions. The position is for 2 years and is funded by the french national agency for research (ANR) A high-pressure environment characterizes our planet. For more than 60 % of the biosphere pressure is greater than 100 bars and it can reach 1000 bars in the deepest sea trenches, like the Marianna's trench. However, in these extreme conditions, a vast biodiversity of adapted micro-organisms (piezophiles) can be encountered. So far, the molecular mechanisms that facilitate proteins function under high pressure remain obscurs. Beside interests to understand fundamental protein folding processes and life evolution, this information is essential to develop biotechnological application from deep sea enzymes. This work will be performed in the framework of a collaborative network including ENS Lyon and IFREMER-UBO in Brest in which a new archaeon from the Pyroccoccus phylum was recently discovered and was called Pyrococcus yayanosii CH1. This microbe is the first obligate piezophile as it is only able to grow under pressure (optimal growth: 98°C and 520 bars). The project is based on the study of two protein families, for which the biochemistry is well handled by the team: large peptidases complexes and lactate/malate dehydrogenase (LDH/MalDH). These proteins play key roles in metabolic adaptation to deep sea ecosystem and allow combining structural approaches (protein crystallography, small-angle scattering...) and biochemical approaches (oligomer stability, enzymatic activity measurements...). The candidate will study the molecular effects of high pressure/temperature by comparing the structural and functional properties of different proteases and LDH/MalDH from Thermococcus and Pyrococcus phylums (including Pyrococcus yayanossi CH1) isolated at various water depths. The ELMA team possesses a fully-fledged wet laboratory for all biochemical steps and the project will benefit from privileged access to large facilities (synchrotron and neutron sources) as well as from latest developments in high-pressure biophysics: high-pressure protein crystallography, for which the ELMA team is a world leader, small-angle x-ray scattering under high-pressure, UV-Visible spectrophotometer and fluorimeter both equipped with a high-pressure vessel. The candidate should have a background in biochemistry with a strong interest in structural approaches or a physico-chemistry background with a strong interest for biophysics. Candidatures, including CV, intention letter and the names and contact information of referees, as well as informal inquiries should be sent to Eric Girard (eric.girard at ibs.fr) and Bruno Franzetti (bruno.franzetti at ibs.fr). Relevant publications from the team: Coquelle et al (2007) Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments. J Mol Biol 374: 547-562. Dura et al (2009) The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea. Mol Microbiol 72: 26-40. Girard et al. (2011). Structure-function perturbation and dissociation of tetrameric urate oxidase by high-hydrostatic pressure. Biophys J 98: 2365-2373. -- *************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA-CNRS-UJF-PSB 41, Rue Jules Horowitz 38027 Grenoble Cedex 1, France Web site:http://www.ibs.fr/ ***************************************************************

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fwd: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15
by Nathaniel Echols 24 Mar '11

24 Mar '11

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> Date: Thu, 24 Mar 2011 16:35:22 -0500 Subject: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15 Dear Colleagues, This is a reminder that the deadline for applications for the 4th annual CCP4 summer school “From data collection to structure refinement and beyond” is April 8. The school will take place June 7-15, 2011 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (the program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2011/ The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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local B-factors
by Priit Eek 24 Mar '11

24 Mar '11

Hi, Talking about B-factors... Being a novice crystallographer I came to a problem: what's the best tool to calculate the average B-factor of a specified region (a domain) in the model, to describe the mobility of chains (or disorder in the crystal) in that region? Regards, Priit

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Multiprocessors/parallel runs keywords
by Jendrek 24 Mar '11

24 Mar '11

Hi, I'm trying to get a grip on what seems to be a multitude of options for running Phenix in multiprocessor/parallel mode. Some of the options/keywords are obvious and easy to find in documentation but other elude me and the posts on the phenixbb make the whole issue even more complicated. So, here is my humble request: Dear Phenix Developers could you please prepare a short summary containing the info concerning running Phenix in multiprocessor/parallel environment for both stable and self compiled developer versions? Even a table with required keywords per program would be a great help... Best regards, Andrzej Lyskowski -- Dr. Andrzej Lyskowski (andrzej[.]lyskowski[(a)]acib[.]at) ACIB Austrian Centre of Industrial Biotechnology GmbH Petersgasse 14, A-8010 Graz, Austria http://acib.at/ c/o IMB Institute of Molecular Biosciences, University of Graz Humboldtstraße 50,III/194, A-8010 Graz, Austria http://strubi.uni-graz.at/ +43 316 380 1993 tel +43 316 380 9897 fax

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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 23 Mar '11

23 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 22 Mar '11

22 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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Re: [phenixbb] "FOM" or HL coeffs from model?
by Dyda 21 Mar '11

21 Mar '11

Phoebe, >How can I get phenix to spit out not just PhiModel but an estimated FOM or fake HL coefficients (without experimental phases - just based on how badly my model agrees with FOBS)? And I'd like the weights in their own personal mtz column(s), not just precombined in a "weighte d phi" column.< can sigmaa do that for you from Fcalc (vector) and Fo (magnitude)? Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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B factor sharpening in twinned maps
by Mary Ho 21 Mar '11

21 Mar '11

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

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changing the project directory
by Charisse Crenshaw 19 Mar '11

19 Mar '11

Hello, I have recently started a project whose folder was located on my desktop. I would like to move that folder off of my desktop as I've heard that having a messy desktop slows down one's computer. I moved the project directory somewhere else, and this resulted in Phenix not being able to find the project (understandably). So I moved it back to its original location and Phenix could then open the project. So, in an X11 shell, I copied the project folder to the new desired location, then changed the output directory in the Phenix main window to that new path. But when I clicked on the project again, the output directory that is indicated changes back to the original path. Now I am looking through the preferences etc for a way to change the path of the project directory within Phenix and I cannot. Can anyone tell me if this is possible and if so, how do I do it? Thanks, Charisse The Salk Institute for Biological Studies

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Refinement Strategy vs. R gap
by Yuri 17 Mar '11

17 Mar '11

Pavel, It seemed like I had to close the GUI window and reopen it for the default (automatic aniso/iso) to take effect. I ran a TLS with 5 groups and ended up with better statistics. Rwork 0.18 Rfree 0.239 -- Yuri Pompeu

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Refinement Strategy vs. R gap
by Yuri 16 Mar '11

16 Mar '11

Hello phenixers, I am refining a liganded structure at 2.1 and I am pretty far into my modeling. Rfree = .265 rwork= .20 My asu has 399 residues one prosthetic group (3178 atoms) and 236 HOH. I just want to do one last refinement round before submission and I am not sure about the strategy I should select as I am running into the following: I- If I refine individuals sites and real space (XYZ) and individual ADP with aniso/iso selection automatic my Rfree goes up slightly and Rwork drops to about .196. I also select optimize x-ray/ADp weight I should say. II- When I choose no XYZ refinement with anisotropic ADP for protein chain only with weight optimization Rwork plummets to 0.15 and Rfree also drops to 0.25. But my gap is now .10 !! I checked my log file and it looks like in default automatic individual ADP phenix.refine is picking all the residues to be anisotropic even though I would not try that at 2.1 A. Could someone point me in the right direction, there is probably something I am overlooking. Thank you -- Yuri Pompeu

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Peptides bonds in cyclic peptides
by Krzysztof Bzymek 16 Mar '11

16 Mar '11

Hi, I've been trying to refine a structure of a protein with a cyclic peptide bound to it. Adding LINK/CONECT to the pdb file works in coot but the bonds are not present after refinement in phenix. I tried creating a param file (I followed recommendations for making ASN/NAG bonds posted here a while ago, but changed the names of connected residues) and included it in refinement, but the bond was not formed and the amino and carboxy groups of respective amino acids were far apart. I also got a message after refinement that a cif file was not specified. What's the solution? Thanks, Chris

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