June 2014 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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how to refine everything except n residues in phenix.refine?
by Murpholino Peligro 22 Oct '14

22 Oct '14

Hi everybody! Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups. Can I tell phenix.refine not to move only those two residues? It should be something like the following lines in the eff file? sites { individual = None torsion_angles = None rigid_body = None remove_selection=resid 45 remove_selection=resid 68 } Thank you very much

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select sphere syntax
by Tanner, John J. 28 Jun '14

28 Jun '14

Is there a way to select a sphere of residues in the phenix.superpose_pdbs command, analogous to the "around" syntax in cns? I tried "within" and "around" in phenix.superpose_pdbs but got "Atom selection syntax error". Thanks. Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: tannerjj(a)missouri.edu<mailto:[email protected]> phone: 573-884-1280 fax: 573-882-2754 http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

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Coot DNA names
by Bradley Hintze 27 Jun '14

27 Jun '14

Hey Folks, Does anybody know a quick way to convert DNA atom names back to PDB standard after coot modifies them to match the ccp4 dictionary? Thanks -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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quick R-value calculation
by Patrick Loll 27 Jun '14

27 Jun '14

I have a structure pulled from the PDB that contains a gnarly, complex ligand, for which I don't have a library. I just want to do a quick R-value calculation +/- ligand, and I don't want to go to the trouble of building and testing a library just for this purpose. Is there some way to induce phenix.refine or phenix.model_vs_data to do the R-value calculation even if it doesn't recognize the nonbonded energy type symbols? Thanks for any tips. Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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seeking help about running SCALEPACK2mtz
by chen c 26 Jun '14

26 Jun '14

Dear PHENIXBBers: I'e got a problem about data processing when running SCALEPACK2mtz. Hope you can give me some advice on that. Here's my problem: I have an .sca file processed by HKL2000 about 4 years ago, I just ran the Scalepack2mtz program in order to transform it into .mtz file. However, the program keeps running. To ensure that the Scalepack2mtz program is ok, I use another .sca file for verification and it turns out that this file for verification is successfully transformed into .mtz file within seconds. I checked the .log file, the program keeps running when there are the following messeages: "Mean acentric moments I from input data: <I^2>/^2 = 2.360 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 9.187 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 52.348 (Expected value = 24.000, Perfect Twin = 7.500) Mean acentric moments I from anisotropically corrected data: <I^2>/^2 = 3.121 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 12.788 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 57.952 (Expected value = 24.000, Perfect Twin = 7.500) " does this means that the .sca file isn't processed properly? I also checked the scale.log file, and there are the following messages: " Shell Summary of observation redundancies: Lower Upper % of reflections with given No. of observations limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19 >19 total 50.00 5.60 5.9 6.1 18.0 15.1 26.9 19.7 8.3 0.0 0.0 0.0 94.1 5.60 4.45 7.9 9.4 13.0 12.9 23.2 27.5 6.1 0.0 0.0 0.0 92.1 4.45 3.88 19.2 5.6 13.3 13.5 20.4 21.9 6.0 0.0 0.0 0.0 80.8 3.88 3.53 31.9 6.5 11.6 11.3 14.9 17.9 5.8 0.0 0.0 0.0 68.1 3.53 3.28 2.4 4.7 11.3 15.3 23.5 34.1 8.7 0.0 0.0 0.0 97.6 3.28 3.08 0.2 3.6 7.0 15.4 23.7 40.1 9.9 0.0 0.0 0.0 99.8 3.08 2.93 0.4 4.4 8.7 16.8 21.1 41.3 7.2 0.0 0.0 0.0 99.6 2.93 2.80 4.2 8.0 12.7 15.2 20.3 33.7 6.0 0.0 0.0 0.0 95.8 2.80 2.69 15.4 9.1 14.0 13.8 19.2 25.2 3.3 0.0 0.0 0.0 84.6 2.69 2.60 31.6 16.2 11.7 14.2 13.7 10.6 2.0 0.0 0.0 0.0 68.4 All hkl 11.8 7.3 12.2 14.4 20.8 27.1 6.4 0.0 0.0 0.0 88.2 " This clearly indicates an ice ring problem in the data-collection process. However, the ice ring problem shouldn't have caused the error during the .sca to .mtz process. In fact, I have use it for structure-solvement, and currently the two R factor is around 30%. However, the large deviation of <I^3>/^3 or <I^4>/^4 do means something wrong. Would you tell me what exact mistakes did I make? Can I use this .sca file for subsequent structure solving and refinement? Great thanks for your help! best regards chen

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Anisotropic B-factor restraints
by Elke De Zitter 26 Jun '14

26 Jun '14

Dear All I'm refining a protein structure with a resolution of 1.25 A, using Phenix GUI version 1.9. I am refining the B-factors for the protein atoms anisotropic and those for the water molecules isotropic. How can I restrain the anisotropic B-factors so that bonded atoms have similar ellipsoids (like the SIMU and DELU commands in Shelx making the atoms moving similarly in direction and amount)? Thanks Elke Elke De Zitter PhD student, KU Leuven Biochemistry, Molecular and Structural Biology Celestijnenlaan 200f - bus 2404, 3001 Leuven Room 00.84, +32 16 3 26530

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Combining phases?
by Yuri 26 Jun '14

26 Jun '14

Dear All, Im struggling with a structure. I have a good native data set with resolution 2.1A and a data set with ok stats collect at low energy trying to extract some anomalous signal from intrinsic sulphur atoms (6/ASU/400aa). Using a model of one of the domains I got a MolRep solution that has somewhat convincing features in the electron density maps some portions of the structure but not in others. I also ran HySS and obtained some coordinates for the 6 sulphur atoms but the map here is uninterpretable. Xtriage suggests the anomalous is only good until about 8A so I am not that surprised. Is there any way I can try to combine my putative MolRep model and phases with the sulphur anomlaous signal and maybe get better maps to build into? If so, how would I do that using PHENIX? thanks for the help -- Yuri Pompeu, Ph.D.

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GRC/GRS Diffraction Methods
by Anastassis Perrakis 26 Jun '14

26 Jun '14

Dear all, I am sorry to send one more post to the already overloaded bb, but please let me remind you for the last time that the deadline for applications for the GRC and the GRS is approaching, and is only three days from now. http://www.grc.org/programs.aspx?id=11654 We are all looking forward to welcome you at Bates College in a month from now, and we do hope for a few more last minute participations: we need all of you to make it as exciting and fun as possible! Best regards, Tassos

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Multiple Metal Sites in Autosol
by Ryan Henry Gumpper 24 Jun '14

24 Jun '14

??Hello All, ?I have a question regarding the metal assignments when using Autosol to process SAD datasets. I am new to field and I want to make sure that I am doing things correctly. My enzyme should contain 2 metal sites, one with Cu and one with Fe. We collected data at the Fe-edge, the Cu-PreEdge, and the Cu-Edge for a comparison. When I tell Autosol to search for 1 Cu site, using the Cu-Edge data, and another heavy atom Fe, it finds 33 sites all Cu with 2 being Fe. Likewise, using the same dataset, when I include S as an additional anomalous scattering moiety, it will find 1 Cu in the correct position and 32 S atoms--my protein does not contain 32 S atoms. Finally, when I include every possibility that was in my crystallization buffer, this includes a fairly high concentration of MgCl2, and I tell it to search for 1 Cu site with the additional heavy atoms being Fe, S, Mg, and Cl, it seems that it is able to assign the Cu correctly, however it now gives Mg coordinated with Cu instead of H2O molecules, and this is not possible. Should I include Mg and Cl in the search? And S? Also, why would it not be finding the Fe? Furthermore, and most importantly, why is it assigning so many heavy atom sites? I am having similar problems with the other two data sets as well. Thank you very much in advance! Regards, Ryan Gumpper

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