- phenixbb - phenix-online.org

distance constrain in phenix
by r n 03 Dec '10

03 Dec '10

Hi I would like to do distance restrain refinement for metal coordination. How can I do metal - protein strict distance restrain refinement in phenix? Thanks ram

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Hydrogen occupancies
by Florian Sauer 01 Dec '10

01 Dec '10

Dear all, I'm currently refining a small protein against 0.96A data using phenix.refine (1.6-486) from the GUI. Refinement without hydrogens yielded Rwork/free of 12.4/14.2. I then added H-atoms with phenix.reduce and switched to individual refinement of hydrogens which dropped the R-factors to 11.3/13.4. After this refinement the occupancies of some hydrogens dropped to 0 which makes me a little concerned. See e.g.: ATOM 752 H LYS A 45 -7.443 2.613 9.537 1.00 4.73 H ATOM 753 HA LYS A 45 -9.707 1.128 9.401 0.55 2.42 H ATOM 754 HB2 LYS A 45 -8.476 2.797 7.435 1.00 10.58 H ATOM 755 HB3 LYS A 45 -9.795 1.948 7.166 0.95 8.70 H ATOM 756 HG2 LYS A 45 -10.840 3.210 8.889 0.00 33.83 H ATOM 757 HG3 LYS A 45 -9.604 4.206 8.775 0.00 33.83 H ATOM 758 HD2 LYS A 45 -11.227 3.615 6.563 0.00 62.10 H ATOM 759 HD3 LYS A 45 -11.508 4.867 7.507 0.00 62.10 H ATOM 760 HE2 LYS A 45 -9.229 5.527 6.985 1.00 83.62 H ATOM 761 HE3 LYS A 45 -9.348 4.488 5.786 0.00 83.86 H ATOM 762 HZ1 LYS A 45 -10.909 5.758 4.853 1.00 99.63 H ATOM 763 HZ2 LYS A 45 -11.131 6.534 6.042 0.35100.44 H ATOM 764 HZ3 LYS A 45 -9.917 6.715 5.257 0.39100.08 H I would like to ask whether it is possible in phenix to group the occupancies to keep them at the same value as the rest of the residue but still refine xyz and isotropic adp of the individual hydrogens? Thank you in advance for your answers, Florian

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wander wall interaction
by subhash bihani 01 Dec '10

01 Dec '10

hi all I am working on a enzyme-ligand complex structure. For some analysis I need to remove wander wall interactions between protein and ligand. How can I do that in Phenix? Something similar to igroup statement in CNS? Thanks in adwance -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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phaser and threads
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ] i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line.... oh, hmmm... i seem to have just got this at the packing function : |python: malloc.c:4591: _int_malloc: Assertion `(unsigned long)(size) >= (unsigned long)(nb)' failed. -Bryan

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building from source : svn_checkout
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-596 from source using --no-gui --no-apps --openmp ] README-DEV mentions ./bin/svn_checkout ... i cannot find this (but i do find bundle_update and recompile). any pointers appreciated. -Bryan

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Refinement of a complex with a symmetric inhibitor lying on the axis of symmetry
by Ina Lindemann 01 Dec '10

01 Dec '10

Hi, I try to refine a crystal structure of a protein - inhibitor complex. The protein is a homodimer and the two molecules have a crystallographic symmetry. The space group is P6122. The symmetric inhibitor binds symmetrically to the protein so that I refine the half of it. The core of the inhibitor is a five-membered ring with a nitrogen lying directly on the axis of symmetry. I achieved to refine this by setting the occupancy to 1.0. And now, here is my problem: Two C atoms of this ring system are bound across the symmetry axis - how could I include this in the refinement? Is there any possibility to generate restraints to the other part of the inhibitor (of the symmetry equivalent)?? Thanks for your help in advance, Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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autosol : unmerged data with input_phase_file
by Bryan Lepore 30 Nov '10

30 Nov '10

dev-595 i gather that autosol will not take unmerged data when the input_phase_file originates from merged data. e.g. in "method #2 for MRSAD". -Bryan

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dev-590 compile from source : -lGLU, -lGL
by Bryan Lepore 30 Nov '10

30 Nov '10

[ dev-590 ] [ gcc 4.4.4 ] [ GNU/Linux 32-bit ] [ Ubuntu 10.10-ish ] * OpenGL/GLUT is of unstable nature* got an error compiling from source (see after sig). i tried using --openmp first, then --openmp --nogui in the same build directory and the error occurs both times. just trying this out, not critical - was interested to know if there's an easy workaround anyone might think of (besides touching GL/GLUT - shudder ). -Bryan /usr/bin/ld: cannot find -lGLU /usr/bin/ld: cannot find -lGL collect2: ld returned 1 exit status scons: *** [lib/gltbx_fonts_ext.so] Error 1

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sculptor : "Wrong alignment format:"
by Bryan Lepore 29 Nov '10

29 Nov '10

(starting a new thread?) trouble with alignment format. tried this : fubar.fas : Sorry: Unknown file(s): fubar.fas fubar.fasta : Sorry: Wrong alignment format: fubar.fasta i compared to one that worked yesterday and its not obvious : first sequence is the target, the pdb sequence is in there (somewhere), i changed a ">sp" to ">gi".... if anyone knows what i'm missing here,... -Bryan

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International Conference on Structural Genomics May 10-14, 2011, Toronto -- registration now open
by Tom Terwilliger 29 Nov '10

29 Nov '10

Dear Colleagues, We are pleased to announce that registration is now open for the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. A substantial number of short talks will be selected from submitted poster abstracts. Also, a limited number of student travel fellowships will be available for travel to this meeting. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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occupancy refinement
by Dalibor Milic 25 Nov '10

25 Nov '10

Dear all! How to refine occupancies of mutually dependent structural fragments found in alternate conformations, but not consecutive in a sequence? E.g. I want to refine occupancies of two alternate conformations of residues 30 and 451 (see below the corresponding parts of a PDB file). Because of the nature of the structural disorder, an occupancy for altLoc A should be strictly the same in both fragments - the same is valid for altLoc B. Of course, the sum of occupancies for altLoc A and B should add up to 1. Thanks for your suggestions, Dalibor Milic ... ATOM 376 N AGLU A 30 23.241 86.975 31.961 0.52 17.13 N ATOM 377 N BGLU A 30 18.971 88.677 32.817 0.48 9.05 N ATOM 378 CA AGLU A 30 23.240 85.507 31.907 0.52 18.89 C ATOM 379 CA BGLU A 30 19.108 87.234 32.991 0.48 10.00 C ATOM 380 CB AGLU A 30 21.848 84.946 32.256 0.52 18.78 C ATOM 381 CB BGLU A 30 17.727 86.562 33.046 0.48 11.01 C ATOM 382 CG AGLU A 30 21.247 85.562 33.524 0.52 26.38 C ATOM 383 CG BGLU A 30 16.935 87.037 34.275 0.48 19.26 C ATOM 384 CD AGLU A 30 20.264 84.659 34.277 0.52 33.36 C ATOM 385 CD BGLU A 30 15.694 86.223 34.542 0.48 26.60 C ATOM 386 OE1AGLU A 30 19.437 83.968 33.620 0.52 31.85 O ATOM 387 OE1BGLU A 30 15.401 85.288 33.762 0.48 33.05 O ATOM 388 OE2AGLU A 30 20.310 84.678 35.535 0.52 29.12 O ATOM 389 OE2BGLU A 30 15.007 86.527 35.538 0.48 30.95 O ATOM 390 C AGLU A 30 23.750 84.946 30.575 0.52 18.22 C ATOM 391 C BGLU A 30 19.976 86.652 31.877 0.48 10.17 C ATOM 392 O AGLU A 30 24.319 83.853 30.534 0.52 19.40 O ATOM 393 O BGLU A 30 20.621 85.606 32.059 0.48 10.67 O ... ATOM 4627 N AALA A 451 31.047 82.837 22.335 0.52 18.30 N ATOM 4628 N BALA A 451 29.107 84.432 26.354 0.48 9.81 N ATOM 4629 CA AALA A 451 31.958 83.502 23.284 0.52 18.73 C ATOM 4630 CA BALA A 451 29.655 85.424 27.274 0.48 9.73 C ATOM 4631 CB AALA A 451 32.880 84.486 22.541 0.52 20.38 C ATOM 4632 CB BALA A 451 30.469 86.474 26.478 0.48 11.60 C ATOM 4633 C AALA A 451 31.176 84.206 24.406 0.52 18.79 C ATOM 4634 C BALA A 451 28.556 86.128 28.089 0.48 6.84 C ATOM 4635 O AALA A 451 30.019 84.593 24.197 0.52 18.25 O ATOM 4636 O BALA A 451 27.441 86.357 27.604 0.48 6.81 O ... -- Dalibor Milic, Dr. Sc. Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia phone: +385 1 460 6377 fax: +385 1 460 6341 e-mail: dmilic(a)chem.pmf.hr

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Re: [phenixbb] occupancy refinement
by Dalibor Milic 25 Nov '10

25 Nov '10

Just an additional comment to my previous e-mail: the refined final value of occupancies in the expression occupancy(AGLU A 30) = occupancy(BGLU A 30) = occupancy(AALA A 451) = occupancy(BALA A 451) were not equal to 0.50 and I got occupancy(AGLU A 30) + occupancy(BGLU A 30) = occupancy(AALA A 451) + occupancy(BALA A 451) < 1.00. Regards, Dalibor -- Dalibor Milic Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia phone: +385 1 460 6377 fax: +385 1 460 6341 e-mail: dmilic(a)chem.pmf.hr

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same origin
by r n 24 Nov '10

24 Nov '10

Hi all I wanted to compare the two models from two data set. I want the MR replacement in same origin to compare their them with respect to the map and model. I tried reforigin in ccp4 , it gave me some error , that I am not aware or not clear. I did tried overlay the two model and rfree is going up. Most likely different hands, so Is there any way to compare the two model and data and modify them in Phenix either reindex or shift the model origin to same in all cases. Thought phenix.xmanip could help, not seen any option to do it command line or in the GUI. I did tried def file, but phenix.xmanip params.def , it complains me that unknown file or keyword? any help will be appreciated. Thanks ram

2 2

sculptor
by Bryan Lepore 22 Nov '10

22 Nov '10

dev-572 I am checking out sculptor, looks pretty cool, but I provided what i thought was a clustal format alignment to sculptor using --verbose, and it reports "Sorry: Wrong alignment format:" that's it. sounds like user error, but i'm not sure where to proceed next. i tried mafft and clustalw2 output for this. a sample of a bit of the top of the .aln is below. -Bryan p.s: shouldn't readseq convert it to .pir? that'd be code 14 PIR/CODATA? CLUSTAL format alignment by MAFFT L-INS-i (v6.833b) gi|16132042|ref --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI gi|157163695|re --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI

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sculptor : alternate conformations
by Bryan Lepore 22 Nov '10

22 Nov '10

dev-586 i'll probably try this anyways, but what is the advice on alternate conformations with sculptor? -Bryan

2 1

Re: [phenixbb] pid's from output
by Thomas C. Terwilliger 20 Nov '10

20 Nov '10

Hi Bryan, I added output such as the following to all autosol/autobuild/ligandfit/automr log files: HOST = sigma.lbl.gov HOSTTYPE = x86_64-linux USER = terwill PID = 27371 This will be available starting with tomorrow's PHENIX build. Thanks for suggesting this! -Tom T 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 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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phenix refinement question
by Katarina Moravcevic 20 Nov '10

20 Nov '10

Hi all, I have only started using PHENIX and have made an interesting observation. If I run my model through PHENIX refine (individual sites, individual ADPs, occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry values (data is to 1.7A). However, if I now take this refined model and run it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21. Can anyone explain why is there such a big difference? Will this be an issue during PDB submission? Any and all comments are appreciated. Thank you all in advance Katarina M.

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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

1 0

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 19 Nov '10

19 Nov '10

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

2 3

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

2 1

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

2 1

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

2 1

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

3 2

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

2 2

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

3 3

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

2 1

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

2 3

autosol/phaser : weak site search and sites
by Bryan Lepore 10 Nov '10

10 Nov '10

dev-572 is there a keyword to disable phaser's weak site search in an autosol run? it seems that using sites=1, max_single_sites=1, sites_file=one_site.pdb isn't doing it. -Bryan

2 1

autosol : space group
by Bryan Lepore 10 Nov '10

10 Nov '10

dev-572 i gave P 2 21 21 data to autosol - seems OK until the .pdb's get written out - they have P 21 21 2 instead. will this be of any consequence - or should i use a standard setting? -Bryan

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autosol : crystal info
by Bryan Lepore 10 Nov '10

10 Nov '10

dev-572 i gather that a .params for isomorphous replacement gets one cell in the crystal_info scope? -bryan

2 1

C and C++
by Hena Dutta 09 Nov '10

09 Nov '10

Dear Members, Sorry for unrelated questions. I thought some of you might have information could be helpful for me. Is there any free website for learning C and C++? Thanks... Hena

2 2

geometry
by Jianghai Zhu 09 Nov '10

09 Nov '10

Hi all, I am refining a 2.75 A structure. The wxc_scale is 0.02, optimize_wxc is false. But the geometry I got doesn't make sense at all. Any explanations? ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 0.617 0.004 0.039 14.275 0.003 4.123 5.8886e-02 1_bss: 0.617 0.004 0.039 14.275 0.003 4.123 5.8886e-02 1_xyz: 3.391 0.059 0.209 16.068 0.010 4.114 1.3055e+00 1_adp: 3.391 0.059 0.209 16.068 0.010 4.114 1.3055e+00 2_bss: 3.391 0.059 0.209 16.068 0.010 4.114 1.3055e+00 2_xyz: 2.435 0.032 0.180 15.961 0.007 4.114 5.4206e-01 2_adp: 2.435 0.032 0.180 15.961 0.007 4.114 5.4206e-01 3_bss: 2.435 0.032 0.180 15.961 0.007 4.114 5.4206e-01 3_xyz: 2.139 0.025 0.191 15.477 0.007 4.114 3.7907e-01 3_adp: 2.139 0.025 0.191 15.477 0.007 4.114 3.7907e-01 ------------------------------------------------------------------------ Thanks. -- Jianghai

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Re: [phenixbb] question on the missing fobs filled maps
by Alexandre OURJOUMTSEV 09 Nov '10

09 Nov '10

Hello, Continuing and confirmating Pavel's last comments: yes, we saw a number of practical cases when non-uniformly distributed missed data, even a small percent, caused great map distortions (some example are listed in our manuscript recently submitted to J.Appl.Cryst). To track this situation, recently we have developed a small python-based program that starting from your MTZ file searches for connected regions of such unmeasured reflections, gives their characteristics and visualizes the regions on the user's request. Presence of such regions may make your maps ugly even when the phases are perfect. For an official release when ready the program will be available at the Web site of the institute; for a time being if you want to test the current version please send me a mail to sacha(a)igbmc.fr With best regards, Sacha Urzhumtsev -----Message d'origine----- De : phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] De la part de Pavel Afonine Hi Fengyun, > I am interesting in that at what completeness of the dataset, will one > use the missing fobs filled map for model building confidently without > too much bias included? I'm not aware of any systematic study on this matter, although at some point I reviewed the available literature. There are numerous examples of how the data incompleteness distorts the map, and literature that discusses this. Interestingly, sometimes much smaller amount of systematically missing reflections, such as plane or cone in reciprocal space, may have much drastic effect than a larger amount of randomly missing data (if you are "lucky" enough it can mask entire structural domain).

2 1

moving user home directories
by Ben Eisenbraun 09 Nov '10

09 Nov '10

Hi PHENIXians, Our local sysadmins moved everyone's home directory from /nfs/home/foo to /nfs/userdocs/home/foo, and it appears to have broken most people's PHENIX projects. Is there a straightforward way to fix this? Poking around in the ~/.phenix/project_db.pkl files, I can see the old paths, but I'm not exactly sure how to rewrite. My brute force attempt with sed was unsuccssful. Thanks. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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Nov 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 08 Nov '10

08 Nov '10

> Dear Users, > > The deadline for Jan/Feb 2010 Collaborative > Crystallography proposals will be *Nov 15, 2010. * > > ---------------------------------------------------------------------------------------- > 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 Jan/Feb 2010 allocation period, > proposals must be submitted by *Nov 15, 2010.* > > The deadline for CC proposals for the time period Mar/April 2010 will be > Jan 15, 2010. > > Regards, > Banumathi Sankaran >

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Fixing a ligand by a symmetry axis
by Simon Kolstoe 04 Nov '10

04 Nov '10

Dear Phenix bb, I have a palindromic ligand bound to my protein that crosses a symmetry axis. Although the head-group that is in close contact with the protein refines beautifully (in phenix..refine version 1.6.4 run from the command line on a mac), the atom closest to the symmetry axis get knocked away from the equivalent atom that it binds to on the other side of the symmetry axis. Is there any way of stopping phenix.refine from refining the atoms closest to the symmetry axis, or should I just manually position the wayward atom in the appropriate orientation prior to my structure deposition? Thanks, Simon

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More trained monkeys please (request for improvements to auto-NCS)
by Kendall Nettles 03 Nov '10

03 Nov '10

Dear PHENIX developers, I am writing to ask about the automated NCS selection procedure. I have a structure with 2 homodimers in the ASU, and there are significant differences in the two monomers that make up teach dimer. When I run automr/autobuild I am very pleased with the result overall, but it does not choose the best NCS groups- it groups all chains to the A chain, instead of one dimer to the other. The result is a helix that is obviously out of place (see attached image). I wonder if this could be fixed by implementing a throw away round of refinement, in order to identify optimal NCS groups? Though it looks like there are only a few areas of significant difference, the structures end up better by grouping one dimer against the other, rather than just the regions that are obviously different. This brings me to my second question. Might it be worthwhile to implement an NCS optimization procedure, which would compare different NCS groups, similarly to the optimize solvents, weights, etc? Kendall Nettles[cid:[email protected].]

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Does phenix have any utility to do the 2mFo-DFc composite omit map calculations?
by zhangh1＠umbc.edu 03 Nov '10

03 Nov '10

Hi, Does phenix have any utility to do the 2mFo-DFc composite omit map calculations (similar to OMIT in CCP4)? Thanks in advance! Hailiang

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phenix.model_vs_data : resolution cutoff from .pdb
by Bryan Lepore 02 Nov '10

02 Nov '10

[ phenix dev-568 ] TIL using phenix.model_vs_data, if the "REMARK 3" records in .pdb are adjusted e.g. to set a resolution limit, e.g REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : [change to whatever high resolution limit] REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.511 phenix.model_vs_data will pick this up and compute the R-factors for that range. Thanks Pavel -bryan

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Riding H
by Jianghai Zhu 02 Nov '10

02 Nov '10

Hi all, If I use the riding H atoms come out of phenix.refine in molprobity, it gives me a decent clash score. But if I strip the H atoms and let molprobity to add H atoms, I get a much worse clash score. I saw the manual of phenix recommends the first method. So what is the cause of the difference here? I know long time ago that phenix and molprobity used different bond length to add the riding H atoms. I don't know what the situation is now. Does phenix.refine refine the riding H atom positions? Thanks. -- Jianghai

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cancel that ...
by Phoebe Rice 01 Nov '10

01 Nov '10

Despite the error messages, it really did make restraints that seem to work. I just didn't realize they'd be in a hidden directory. Can I put in a request for no hidden defaults? They make me feel like a trained monkey. thanks, Phoebe

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error in making links
by Phoebe Rice 01 Nov '10

01 Nov '10

Hi BB, I wanted to run phenix on a structure from the database with covalent serine-DNA links, 1zr4. The "ready-set" feature to prepare restraints from the pdb link records sounded lovely, but fails with the message "Error interpreting command line argument parament definition: "1ZR4.link.edits" RuntimeError: Unexpected end of input" This happens with either version 1.6.4-486 or a nightly build installed a few weeks ago (phenix 551; installed on 10/7/2010.) Am I asking to much to get nice Ser-DNA links without sweating blood to read the fine print? thanks, 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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refine : "merged" in .def
by Bryan Lepore 29 Oct '10

29 Oct '10

[ dev-564 on GNU/Linux ] why does phenix - apparently - keep putting the label "merged" in output .def's, when neither the input .def or .mtz has this label - and what generally is the significance? the .mtz has separate Bijvoets, and I's. e.g: input .def: (concise) labels = "I(+),SIGI(+),I(-),SIGI(-)" label = "R-free-flags" output .def: labels = "I(+),SIGI(+),I(-),SIGI(-),merged" label = "R-free-flags" i re-checked the .mtz lacks "merged" (not shown). -bryan

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Autobuild error - bash/dash/sh
by Stephen Graham 29 Oct '10

29 Oct '10

Hi there, Apologies if this has been reported before, but the autobuild job I tried to run last night failed after a short while... The job was started from the command line using: phenix.autobuild data=../mydata_free.mtz seq_file=../protein.fasta map_file=../ccp4i/protein_phaser.1_parrot2.mtz input_map_labels='parrot.F_phi.F parrot.F_phi.phi None' And it got to the point where it was trying to submit the three jobs before it died as follows: Splitting work into 3 jobs and running with 1 processors using sh background=False in /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0 Starting job 1...Log will be: /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.log *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'sh /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1' /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.sh: 5: Syntax error: Bad fd number ******************************************************************************** *************ERROR ENDING ******************* I think the problem might be that the RUN_FILE_1.sh script seems to use a bash command/redirection that is not implemented in plain old 'sh' spec, and thus not supported by dash (the lean version of sh that ships with ubuntu)? If I change the #! line of RUN_FILE_1.sh to call /bin/bash rather than /bin/sh the script seems to run to completion... Is there any easy way to change the script template to use /bin/bash or remove the offending command? I'm running phenix dev-550 on an x86 ubuntu 10.10 machine. Thanks, Stephen P.S. The reason I'm trying to run autobuild from the command line rather from the GUI is that the GUI seems to crash every time I give autobuild a sequence file in either the FASTA or PIR format. Is there another format I should be using? -- 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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