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phenix.elbow with gamess
by William Scott 19 Nov '10

19 Nov '10

The command phenix.elbow --games --smiles="CCO" now fails (1.61 and most recent nightly), but works in an older version of phenix (1.6). Do I need to change input syntax? (I've tried both with older and more recent 32 and 64-bit gamess). Thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ PS: Here is the error output 0:07 WriteGAMESSInput WriteGAMESSInput WriteGAMESSInput WriteGAMESSInput Write 0 -3.5160526786 -17.580263393 1 4.03396746237 20.1698373118 2 -2.978694357 -14.893471785 3 2.92412711501 14.620635575 4 -3.25561740601 -16.2780870301 5 3.2398773487 16.1993867435 [-3.5160526785963961, 4.0339674623667952, -2.9786943570030093, 2.9241271150050951, -3.2556174060111247, 3.2398773486970533] Traceback (most recent call last): File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/command_line/builder.py", line 1691, in <module> run() File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/command_line/builder.py", line 1583, in run call_back_function=call_back_function, File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/command_line/builder.py", line 874, in post_process call_back_function=call_back_function, File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/utilities/optimisation_manager.py", line 514, in optimisation_manager function(*args, **kwds) File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/quantum/GAMESSMixins.py", line 403, in WriteGAMESSInput points, outl = get_density_grid(self) File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/quantum/GAMESSMixins.py", line 190, in get_density_grid assert 0 AssertionError

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pid's from output
by Bryan Lepore 19 Nov '10

19 Nov '10

any way to get pid's of a given phenix process from their output (or any other tricks)? e.g. tried lsof, etc., dug through some title.dat, correlating date.. this would be helpful e.g. when a bunch of autobuilds start after an automr with an expired pid. -Bryan

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relationship between B factors and Koff
by Sebastiano Pasqualato 19 Nov '10

19 Nov '10

Hi all, I have a crystallographical/biochemical problem, and maybe some of you guys can help me out. We have recently crystallized a protein:protein complex, whose Kd has been measured being ca. 10 uM (both by fluorescence polarization and surface plasmon resonance). Despite the 'decent' affinity, we couldn't purify an homogeneous complex in size exclusion chromatography, even mixing the protein at concentrations up to 80-100 uM each. We explained this behavior by assuming that extremely high Kon/Koff values combine to give this 10 uM affinity, and the high Koff value would account for the dissociation going on during size exclusion chromatography. We have partial evidence for this from the SPR curves, although we haven't actually measured the Kon/Koff values. We eventually managed to solve the crystal structure of the complex by mixing the two proteins (we had to add an excess of one of them to get good diffraction data). Once solved the structure (which makes perfect biological sense and has been validated), we get mean B factors for one of the component (the larger) much lower than those of the other component (the smaller one, which we had in excess). We're talking about 48 Å^2 vs. 75 Å^2. I was wondering if anybody has had some similar cases, or has any hint on the possible relationship it might (or might not) exist between high a Koff value and high B factors (a relationship we are tempted to draw). Thanks in advance, best regards, ciao s -- 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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automr/phaser : b-factors
by Bryan Lepore 18 Nov '10

18 Nov '10

does (or can) phaser use the search probe B-factors in any way? -Bryan

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CRYST card being changed
by Nino Campobasso 18 Nov '10

18 Nov '10

Phenix developers, When I run a refinement, it appears that the CRYST card is not being written as expected by programs like pymol and coot. I'll start with a file that has C 1 2 1 and phenix.refine will write out C2 . If I attempt to view symmetry related molecule within coot or pymol, these programs complain that there is no symmetry op. If "fix" the spacegroup in the CRYST line, pymol and coot are happy and generate the related molecules. Best, Nino

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autobuild : rigid?
by Bryan Lepore 18 Nov '10

18 Nov '10

dev-572 my understanding of the autobuild<->refine keyword table on the website is that there's no rigid body available through autobuild - is that right? -Bryan

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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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