- phenixbb - phenix-online.org

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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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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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

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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 09 Nov '10

09 Nov '10

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

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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

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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).

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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 01 Nov '10

01 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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