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reflection file converter
by r n 17 Nov '10

17 Nov '10

Hi I did tried reflection file converter in phenix. I do have the anomalous data, like to keep all anomalous difference and also merged F and FreeR for refinement. Phenix GUI give me an warning message that "File are not suitable for amplitudes change them as F or leave them as Intensities" Also have hard time to convert them in command line, Is there any auto script that can work similar to scaelpack2mtz , which keeps all I+, I- and F , SigF, Rfree for refinement. Converted using Phenix.refine , that keeps separate I+, I- and Rfree+, Rfree-. Thanks ram

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link restraints for modified nucleotides in RNA
by Gerwald Jogl 17 Nov '10

17 Nov '10

Hi All, I am refining several modified nucleotides in ribosomal RNA (N2-methyl-guanosine and similar). While the restraints generation with phenix.reel work quite well, I am unable to get the phosphate oxygen restraints applied properly. Phenix.refine recognizes the links but for some reason the phosphate groups come out quite distorted... For example, angles after refinement: O3 (1) - P (2, modified) - OP2 (2) = 80 deg and O3 (1) - P (2, modified) - OP1 (2) = 127 deg Here is part of the phenix.refine log on reading the coordinates: Chain: "A" Number of atoms: 32526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1513, 32526 Unusual residues: {'MA6%rna3p': 2, '5MC%rna3p': 3, '5MC%rna2p': 1, '7M G%rna3p': 1, '2MG%rna3p': 1, 'UR3%rna2p': 1, 'M2G%rna3p': 1, '4OC%rna3p': 1} Classifications: {'undetermined': 11, 'RNA': 1502} Modifications used: {'5*END': 1, 'rna3p': 1318, 'rna2p': 195} Link IDs: {'rna3p': 1318, 'rna2p': 194} Chain breaks: 1 I am at a loss about how to fix this as all links and restraints seem to be in place. Many thanks for advice, Gerwald

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phaser and automr
by Bryan Lepore 16 Nov '10

16 Nov '10

IIUC, phaser keywords cannot be provided to phenix.automr - is that right? i.e. if that's the case, then i ought to run phenix.phaser. -bryan

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automr : [1] MAP_COEFFS [2] output pdb's of ensemble
by Bryan Lepore 16 Nov '10

16 Nov '10

dev-572 [1] in automr, i do not understand why only the last MR.MAP_COEFFS.n.mtz is written- e.g. i don't get 1-9 if 10 models are requested as output. (MR.[1-n].mtz are written ok). [2] when using an ensemble, i gather that the output is *hardwired* for the best rmsd model - i.e. there are no keywords to write out all parts of the ensemble. (i know i can run pdbset for them, but anyways...) -Bryan

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automr : *refinement* resolution limit keyword?
by Bryan Lepore 16 Nov '10

16 Nov '10

[ dev-572 ] i'm wondering if users can set the *refinement* resolution limits in automr? the webpage suggests this, but it wasn't clear to me. i can set the search resolution fine, however by default as indicated, all data is used - and the only other keyword i see that would at all be relevant is the building resolution. -Bryan

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refine : annealing temperature
by Bryan Lepore 13 Nov '10

13 Nov '10

just wondering if the annealing temperature in phenix is absolutely the same as in cns. -Bryan

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Question about restraints
by Schubert, Carsten [PRDUS] 13 Nov '10

13 Nov '10

Hi, I was wondering what the default values for restraints in reel/elbow represent in terms of 'tightness' for lack of a better word. I am trying to tighten up the geometry of a badly behaving ligand and want to avoid over tightening. What is the consensus out there what kind of ESDs represent a 'loose' 'medium' and 'tight' restraint for bond, angle, dihedral, planar and chiral restraints. Thanks Carsten

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automr : ensemble on command line
by Bryan Lepore 12 Nov '10

12 Nov '10

dev-572 i keep getting this error : The number of entries in identity_list ([80.0, 80.0]) needs to be the same as the number of entries in ensemble_1.coords (1) on the command line, i specify the ensemble as : coords='MR_probe_5_match_to_9.pdb MR_probe_9.pdb' identity='80 80' it gets picked up like this : ... ensembleID = "ensemble_1" copies_to_find = None coords = "MR_probe_5.pdb MR_probe_9.pdb" identity = 80 80 ... i tried using quotes or not, and rmsd. i'm using "\" for the shell - what am i missing here? any clues to look for? -Bryan

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Two Post-Doc opportunities in cell biology and biochemistry in Milan, Italy
by Sebastiano Pasqualato 11 Nov '10

11 Nov '10

Hi all, I'm sending this on behalf of a colleague, so please reply to giorgio.scita(at)ifom-ieo-campus.it if interested. PS: to those concerned, apologies for the double post. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

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phenix.autosol : scala unmerged ok?
by Bryan Lepore 10 Nov '10

10 Nov '10

[ phenix-dev-572 ] i gave autosol unmerged I, SIGI, M/ISYM from scala for a derivative and a native. from the docs, it appears this is automated. but it appears that solve thinks its scalepack_merge, and other things (LAST.LOG) what keywords should i consider here? should i just use scalepack format? -bryan

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