- phenixbb - phenix-online.org

are the rigid_body group shifts cummulative or stepwise?
by Scott Classen 30 Mar '11

30 Mar '11

i.e. do the translation & rotation values reported in each rigid body step in the log file represent the TOTAL shift from the initial pre-RB model or just the shift for that particular step? Thanks, Scott

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Same enzyme, different space groups ?
by Yuri 29 Mar '11

29 Mar '11

Hello everyone, I was comparing 2 data sets I have and when I run Xtriage I noticed the following: a) for one crystal (data processed in P 4 2 2) | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ------------------------------------------------------------------------------------ | P 41 21 2 | 24 | 0.03 | 1.30 | 0 | 2 | 0.000e+00 | | P 43 21 2 | 24 | 0.03 | 1.30 | 0 | 2 | 0.000e+00 | | P 42 21 2 | 22 | 0.03 | 1.27 | 0 | 4 | 7.187e-02 | | P 4 21 2 | 18 | 0.01 | 1.21 | 0 | 8 | 3.035e-01 | | P 41 2 2 | 6 | 0.11 | 1.59 | 0 | 20 | 9.065e-01 | | P 43 2 2 | 6 | 0.11 | 1.59 | 0 | 20 | 9.065e-01 | | P 42 2 2 | 4 | 0.13 | 1.57 | 0 | 22 | 9.784e-01 | | P 4 2 2 | 0 | 0.00 | 0.00 | 0 | 26 | 1.210e+00 | ------------------------------------------------------------------------------------ b) the other crystal, of the same enzyme (data scaled in P 43 21 2) x triage tells me this crystal is in P 43 21 2. | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 4 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 4 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 41 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 41 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 42 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 42 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 43 2 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | | P 43 21 2 | 0 | 0.00 | 0.00 | 0 | 2 | 0.000e+00 | ----------------------------------------------------------------------------------- My understanding is that P 43 21 2 should have 0 systematic absences (if I am wrong, please point it out) My questions are: what is really my space group? Or should I say space groups, if indeed I have two different space groups. How do I nterpret the scores? Could it all be a function of the space group they were processed in? -- Yuri Pompeu

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Target weight optimization (wxu_scale and wxu)
by Zhang yu 29 Mar '11

29 Mar '11

Dear Phenixer, What is the real meaning of the 'wxu_scale' and 'wu'? (scale factor for X-ray/ADP_weight: wxu_scale ADP weight scale: wu) During ADP refinement, it is suggested to refine the 'wxu_scale', what if I change the value of 'wu'? Thanks Yu

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Split Occupancy of a ligand and water
by Brandon Goblirsch 29 Mar '11

29 Mar '11

Hello, Currently I am have a structure which has a ligand bound at less than full occupancy. The ligand in this cause is covalently linked to a CYS residue in the enzyme active site. When the ligand is not present, there are two well conserved waters in the active site in its place. Overall, I have a same space, split occupancy issue. The problem I am having now in phenix 1.7.460 is that I want to refine (simultaneously) these water positions superimposed on the bound ligand position (as both have less than 100% occupancy). However, upon refinement, the waters are always "kicked out" of position and are not allowed to overlay with atoms within the bound ligand. Does anyone know how to get phenix.refine to accept the water and ligands occupying the same coordinate space. Obviously setting the ligand and water positions to sub 100% occupancy does not do the trick. Thanks for any help!! Brandon -- Brandon Goblirsch Research Assistant-Wilmot Lab Biochemistry, Molecular Biology and Biophysics 5-230 Nils Hasselmo Hall Minneapolis, MN 55455 (612)624-0141

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anomalous difference map
by Jason 28 Mar '11

28 Mar '11

Hello Everyone, I have an old question about how to create anomalous difference map. Facts: 1) Synchrotron Fluorescence scan indicates the heavy atom definitely presents in my protein (my control is a second protein with the same ligand showed no absorbance spectrum) 2) xds processed mtz file 3) Data resolution ~ 3 angstron 3) molecular replacement solved apo structure protein.pdb using phenix.refine 4) phenix.maps to generate anomalous map (phenix.refine will also generate it, but let's leave it aside for the moment) Questions: When I load the mtz file to phenix.maps GUI, the mtz label pulldown menu indicates 4 possible choices for the column to use:(1) IMEAN, SIGIMEAN (2) I(+), sigI(+), I(-), sigI(-) merged (3) F(+), sigF(+), F(-), sigF(-) merged (4) F, sigF, Dano SigDano. I have tried the choices of (2) (3) and (4). However, there is barely any anomalous signal at 4sigma, which makes me wondering if something is not right. The first thing coming to my mind is the mtz labels: I(+), sigI(+), I(-), sigI(-) merged. What does merged mean? Could this be the reason? Other issues that could causing the trouble? Thank you all. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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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 26 Mar '11

26 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 26 Mar '11

26 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 25 Mar '11

25 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 25 Mar '11

25 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 25 Mar '11

25 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 25 Mar '11

25 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 25 Mar '11

25 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 25 Mar '11

25 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 24 Mar '11

24 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 24 Mar '11

24 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 23 Mar '11

23 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 22 Mar '11

22 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 17 Mar '11

17 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 17 Mar '11

17 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

2 1

Only one solution in AutoMR with very negative LLG
by Zhang yu 17 Mar '11

17 Mar '11

Hi, I am working on a DNA-protein complex, the protein apo structure is already known. Recently I got a dataset of the DNA-protein complex, I tried to find a solution by autoMR in Phenix with the known protein coordinate as template. I got only one solution with very negative LLG (around -4000), and after rigid body refinement, the both Rwork and Rfree is around 0.55. Was there anyone in the same situation as me? What does that mean if there is just one solution while with very high negative LLG? Thanks

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Need help in refining my twinned P6322(apparent) dataset
by John Pak 16 Mar '11

16 Mar '11

Hey Phenix community, Here are the details of my current situation - any assistance in the matter would be greatly appreciated as I've been struggling mightily for the past month trying to get this structure refined (to no avail). Details: -3.0 angstrom dataset from a membrane protein crystal -reduced in a P3 Bravis lattice using HKL2000 -Pointless and Xtriage suggest P622 symmetry -Solved structure via MR - ran Phaser in all P622 based space groups, found 1 convincing solution in P6322 (LLG ~110) which makes biological sense (1 monomer in ASU that lies on the screw axis to recapitulate the biological trimer) -31% sequence identical search molecule -no pseudotranslation (via Xtriage) Xtriage suggests that the P6322 dataset is nearly perfectly twinned (twin fraction = 0.49). Mindful of the fact that there are no twin operators for P6322, I'm thinking that the true space group is P321, P312 or P63 and I've tried a number of things listed below: 1. Refined in P6322 (simulated annealing+individual B). Missing side chains and incorrectly modelled loops apparent in maps. Start R=0.49, Rfree=0.5. Refinement stalls at R=0.41, Rfree=0.45 after building. 2. Ran Phaser in P312 (using unrefined model) - no solution. 3. Ran Phaser in P321 (using unrefined model). One nice solution (LLG ~220) - lattice looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage (simulated annealing + individual B) results in R=0.38, Rfree=0.41 (no rebuilding performed). 4. Ran Phaser in P63 (using unrefined model). Three solutions (LLGs all ~210) - solution #3 looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage of solution #3 gives R=0.37, Rfree=0.40 (no rebuilding performed). Solutions #1 and #2 do not give packing arrangements that look like the P6322 solution. Twin refinement of Sol 1 and 2 give higher R factors. So I'm at a loss as to which space group my crystal truly belongs to, and where I should be focusing my refinement. The maps all look similar before and after DM. Thanks for any assistance or recommendations that you might have! -- John E. Pak, Ph.D. Postdoctoral Associate, Stroud Lab Department of Biochemistry& Biophysics UCSF MC2240 Genentech Hall Room S414 600-16th St. San Francisco, CA 94158-2517 Lab #: 415-476-3937 Fax #: 415-476-1902 Cell #: 415-215-0048

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fwd: Re: Need help in refining my twinned P6322(apparent) dataset
by Nathaniel Echols 16 Mar '11

16 Mar '11

---------- Forwarded message ---------- From: "Van Den Berg, Bert" <Lambertus.VandenBerg(a)umassmed.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Tue, 15 Mar 2011 08:01:42 -0400 Subject: Hi John, How do the maps look for cases 3 and 4? Are they great or are there obvious things to correct? Does your model have the correct sequence or is it that of the search model? I’m asking because your R’s seem reasonable to me after a first round of refinement and using a 30% identical search model for MR. So maybe there is no problem? Bert On 3/15/11 2:55 AM, "John Pak" <john.pak(a)msg.ucsf.edu> wrote: Hey Phenix community, Here are the details of my current situation - any assistance in the matter would be greatly appreciated as I've been struggling mightily for the past month trying to get this structure refined (to no avail). Details: -3.0 angstrom dataset from a membrane protein crystal -reduced in a P3 Bravis lattice using HKL2000 -Pointless and Xtriage suggest P622 symmetry -Solved structure via MR - ran Phaser in all P622 based space groups, found 1 convincing solution in P6322 (LLG ~110) which makes biological sense (1 monomer in ASU that lies on the screw axis to recapitulate the biological trimer) -31% sequence identical search molecule -no pseudotranslation (via Xtriage) Xtriage suggests that the P6322 dataset is nearly perfectly twinned (twin fraction = 0.49). Mindful of the fact that there are no twin operators for P6322, I'm thinking that the true space group is P321, P312 or P63 and I've tried a number of things listed below: 1. Refined in P6322 (simulated annealing+individual B). Missing side chains and incorrectly modelled loops apparent in maps. Start R=0.49, Rfree=0.5. Refinement stalls at R=0.41, Rfree=0.45 after building. 2. Ran Phaser in P312 (using unrefined model) - no solution. 3. Ran Phaser in P321 (using unrefined model). One nice solution (LLG ~220) - lattice looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage (simulated annealing + individual B) results in R=0.38, Rfree=0.41 (no rebuilding performed). 4. Ran Phaser in P63 (using unrefined model). Three solutions (LLGs all ~210) - solution #3 looks very similar to P6322 crystal packing. Twin refinement in phenix using operator suggested by Xtriage of solution #3 gives R=0.37, Rfree=0.40 (no rebuilding performed). Solutions #1 and #2 do not give packing arrangements that look like the P6322 solution. Twin refinement of Sol 1 and 2 give higher R factors. So I'm at a loss as to which space group my crystal truly belongs to, and where I should be focusing my refinement. The maps all look similar before and after DM. Thanks for any assistance or recommendations that you might have! -- John E. Pak, Ph.D. Postdoctoral Associate, Stroud Lab Department of Biochemistry& Biophysics UCSF MC2240 Genentech Hall Room S414 600-16th St. San Francisco, CA 94158-2517 Lab #: 415-476-3937 Fax #: 415-476-1902 Cell #: 415-215-0048

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Mar 15, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 15 Mar '11

15 Mar '11

Dear Users, The deadline for May/June 2011 Collaborative Crystallography proposals will be *Mar 15, 2011.* ---------------------------------------------------------------------------------------- Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for May/June 2011 allocation period, proposals must be submitted by *Mar 15, 2011.* The deadline for CC proposals for the time period July/Aug 2011 will be May 15, 2011. Regards, Banumathi Sankaran

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Jan 15, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 15 Mar '11

15 Mar '11

Dear Users, The deadline for March/April 2011 Collaborative Crystallography proposals will be *Jan 15, 2011.* ---------------------------------------------------------------------------------------- Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for March/April 2011 allocation period, proposals must be submitted by *Jan 15, 2011.* The deadline for CC proposals for the time period May/June 2011 will be March 15, 2011. Regards, Banumathi Sankaran

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B-factor discrepancy
by Yuri 15 Mar '11

15 Mar '11

I am refining a single-mutant structure at 2.1 A. The native was solved years ago by heavy atom phasing. The reported average B-factors for alpha carbons especially of the original structure were significantly lower than the ones I am seeing. around 15 vs. around 25. Has anyone any idea if this is perfectly fine and its simply something intrinsic to my crystals? Also at this resolution, should I try to refine any residues at all anisotropically? Thanks for the guidance

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XYZ refinement vs individual sites refinement
by Yuri 14 Mar '11

14 Mar '11

I am new to phenix and I am trying to probe two residues that are putative H-bond partners, after refinement they seem to be put in orientations that would make it impossible for them to be interacting with a ligand. My SA composite omit map may suggest that one of the Asn could be in a different position. My question: If I manually change its conformation is it wise to keep its position fixed during refinement to see what the new maps would look like? If so where would I do that under the real space or individual sites tab on GUI phenix? I am not sure what these 2 tasks accomplish exactly. Any guidance would be appreciated. Thanks Yuri Pompeu

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Fwd: XYZ refinement vs individual sites refinement
by Yuri 14 Mar '11

14 Mar '11

Thats better! thank you

1 0

most appropriate map for ligand fitting/interaction with FMN
by Yuri 13 Mar '11

13 Mar '11

I am refinig a structure at 2.1 A. I have 2 questions: a) Is the best way to identify a ligand refining the protein and water molecules and at the end looking at the 2mfo-dfc and mfo-dfc maps? Or looking at a SA composit omit map? b) In almost every map i look at during refinement I see density that smears/joins my ligand (cyclopentenone type molecule) and flavin's isoalloxazine ring. Has anyone ever seen that? they seem to be 3.1 A apart? Thanks -- Yuri Pompeu

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Elbow problem
by Jerome Nwachukwu 12 Mar '11

12 Mar '11

Hi all: For some reason, phenix.elbow converts a specific double-bond (C=C) in my ligand to a single bond (C-C) and therefore generates a wrong .cif file. Is there away to avoid or correct this problem? Thank you, -Jerome Jerome C. Nwachukwu, PhD Kendall Nettles' Lab Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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Binary Installation failure on Ubuntu
by Katherine Sippel 12 Mar '11

12 Mar '11

Hi all, I am trying to install the latest nightly build (dev-694) using the Kernel 2.6 (64-bit; Fedora Core 3) binary. The OS is Ubuntu 10.10 installed as a dual boot through Wubi. I get as far as configuring PHENIX components at which point it heaves out a binary.log file. I can send the whole file to anyone whose interested but it's a bit too large for the bb. The juicy bit is as follows... Could not find platform independent libraries <prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site How can I determine which libraries are missing? Thanks for any help you can provide, Katherine

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Average maps (*not* NCS averaging)
by Stephen Graham 11 Mar '11

11 Mar '11

Hi there, I'd like to average 2Fo-Fc maps from 2 (approximately) isomorphous data sets (one with ligand, one without) to see whether I get better density for some of the noisier bits of the structure. I don't want to do any kind of solvent flattening, histogram matching, cyclical averaging, etc; I just want to sum the equivalent pixels and divide by 2. Is it possible to do this easily using any of the phenix tools? It seems like all the required plumbing is there with get_cc_mtz_mtz or superpose_maps, but I can't find a phenix utility for averaging two superposed maps. Thanks, Stephen -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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Re: [phenixbb] [ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 11 Mar '11

11 Mar '11

Sorry, I forgot to mention about what is the .obj file I need. It is a pure ASCII geometric description of a polyhedra. Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file It looks rather easy to parse compared to some VRML file, for example. Thanks, F. Francois Berenger wrote: > Hello, > > What are the good software to do this? > > I already know of Pymol and Jmol. > > Both can export the result to a .obj file, which is interesting for > later processing. > > However, Pymol's algorithm is not exactly what Connolly described, > cf. > http://www.mail-archive.com/[email protected]/msg00179.html > > Also, Pymol will save the surface with some translation and rotation > which are not present in the PDB read in, which is a real pain. > > For Jmol, sometimes the surface is not a closed polyhedra, so > it is kind of useless for my purpose. > > I know of MSMS, but I don't think it is that robust (I read some source > code where someone was using MSMS, the source code had many dirty things > in order to try handling the apparently many cases where MSMS was > crashing). > > Is there something freely usable for research, using beta shapes > internally, for example? That should be a robust approach. > > A robust software would be much appreciated (not crashing, whatever > the PDB we give it as input). > Open source and not in Fortran would be heaven. ;) > > Thanks a lot for suggestions, > F.

1 0

Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 11 Mar '11

11 Mar '11

(was posted on CCP4 bb also) Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/[email protected]/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.

1 0

automr renumbered all residues to 0 for final solution in dev-674
by Francis E Reyes 11 Mar '11

11 Mar '11

Is this fixed in a later version? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

1 0

ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 10 Mar '11

10 Mar '11

Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 10 Mar '11

10 Mar '11

Hi Pavel, What I meant it was just that the 2mFo-2DFc map looks really great and corroborates experimental data as far as the stereochemistry. But I dont understand ehy the carbonyl moiety of the ligand would be where it is now, no "driving force to be here". And when I look at my averaged kick and SA omit map it looks ambiguous. Any help?

1 0

ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 10 Mar '11

10 Mar '11

Hello everyone, I have this strucuture I solved by Molecular replacement. It is a single mutant of previously solved enzyme. I started refining it and fit the ligand in a way that gives me the experimental stereochemistry. The final map 2mFo-2DFc looks great. After further examination I noticed, I have a carbonyl that does not seem to be bound to anything !!! I started looking at my average kick and SA composit omit-map prior to modeling in the ligand and now I am really lost. Could anyone help? Thank you

2 1

Important change in phenix.refine output: MTZ file with data and map coefficients
by Pavel Afonine 05 Mar '11

05 Mar '11

Hi Everyone, starting development version dev-686: http://www.phenix-online.org/download/nightly_builds.cgi phenix.refine does not output *map_coeffs.mtz file. Instead, it creates prefix_serial.mtz file (example: lysozime_001.mtz) containing four sections: - section 1: Original input data (Iobs or Fobs, and HL coefficients if provided) and flags (as supplied in input); - section 2: Experimental data used in refinement (labels: F-obs-filtered, SIGF-obs-filtered). This can be different from "Original data" due to Iobs->Fobs conversion (if input data are intensities) and outliers filtering; - section 3: Contains total model structure factors (labels: F-model, PHIF-model) used everywhere in refinement (for the formula, see: http://www.phenix-online.org/documentation/fmodel.htm). In the future, this section might be extended to explicitly list all contributions to Fmodel, such as Fcalc (corresponding to atomic model), Fbulk (bulk solvent contribution), and so on. - section 4: Fourier map coefficients (exactly the same as used to be in *map_coeffs.mtz file). This change is meant to reduce the confusion when people tended to use *map_coeffs.mtz file for refinement and PDB deposition, and facilitates the reproduction of refinement statistics (R-factors, for example). Also, thanks to Jeff Headd, by default phenix.refine now converts input intensities (Iobs) to amplitudes (Fobs) using French & Wilson method (Acta Cryst A34, 517, 1978), so no need to run a specific program (Truncate, for example) to do this. To see the content of a MTZ file use phenix.mtz.dump command: phenix.mtz.dump data.mtz Pavel.

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Geometry problem with sugars refined in phenix
by Tirumala Kumar Chowdary 03 Mar '11

03 Mar '11

Hi, I have refined a structure with NAGs linked to ASNs at 3 places in my structure. I used the right link definitions and the NAG definitions are from Phenix library. Phenix refined all the sugars right and made the right links between the NAGs. However, while submitting, PDB found problem with the geometry of NAGs linked to the ASN at two places. This is the issue -the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A #1670 are on a plane and the C1 atom center is far off to be tetrahedral. Please, verify the chirality of C1 and provide the correct coordinates if necessary.- Any ideas on how to fix the geometry of these sugars will be of great help. Regularization and real space refine in Coot is not working or I don't know how to do it. I am looking for alternative ways to fix this problem. Thank You Tirumal

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