- phenixbb - phenix-online.org

Same enzyme, different space groups ?
by Yuri 28 Mar '11

28 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 28 Mar '11

28 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 28 Mar '11

28 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 25 Mar '11

25 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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