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Re: [phenixbb] Question about precedence of command line parameters vs. .def file
by Ralf W. Grosse-Kunstleve 14 Aug '07

14 Aug '07

Hi Carsten, > I see how the loading of both pdb files can be a desired feature, but I > also recall reading somewhere that command line params take precedence > over .def files, which in turn takes precedence over defaults. There > seems to be some deviation from that philosophy. Each parameter has a bunch of associated attributes to control the behavior. The attribute that causes trouble here is .multiple=True. It means that you can specify multiple values. Values accumulate in the order given. .multiple=True is used in many places and in general this feature works well, but in the case of the pdb file name it sometimes causes confusion. Unfortunately I don't see an obvious way around this. It would be possible to support something like pdb.file_name==your.pdb, where == means discard all accumulated values and start over with the new value, but that wouldn't be very intuitive. Or we'd have to stop supporting reading of multiple pdb files. I wonder if you could achieve your goals with a different approach. The idea is not to use the .def files produced by phenix.refine. I'm guessing you're doing this because they contain all your accumulated customizations defined via the command line. Could you organize your workflow to accumulate the customizations in a separate file, then pass that file as another argument? E.g.: Content of "params" file: refinement.main.macro_cycles=5 refinement.main.high_resolution=3 phenix.refine my.pdb params > This also would help future automation we are implementing, because > it would eliminate the need to read and parse an existing .def. file. Parsing and rewriting a .def file is very easy from Python. If you have phenix, you also have both Python and a parameter file parser and writer. The "phil" parser/writer is documented in this newsletter article: http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf I could help you getting started if that's an interesting alternative. If you can think of a more intuitive way of handling the interaction of parameters with multiple values and command-line parameters, please let me know! Ralf

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Question about precedence of command line parameters vs. .def file
by Schubert, Carsten [PRDUS] 14 Aug '07

14 Aug '07

Hi, I have a question / request about parameters defined on the command line vs. defined in the .def file are handled. Specifically the input.pdb.file_name parameter. I noticed that if I have already a input.pdb.file_name defined in the .def file and call phenix.refine with another pdb file, both files are loaded. If both pdb files represent the same protein in different stages of refinement that obviously causes the job to fail due to close non-bonding interactions. I see how the loading of both pdb files can be a desired feature, but I also recall reading somewhere that command line params take precedence over .def files, which in turn takes precedence over defaults. There seems to be some deviation from that philosophy. For me this is more a work-flow issue (which becomes important if one does to many structures per day ...) than a bug. I'd really like to minimize the time spend on editing the def file and just define new job parameters from the command line and have the def file fill in the missing bits. This also would help future automation we are implementing, because it would eliminate the need to read and parse an existing .def. file. There are ways around this but not as clean, but that is another matter .... Would it be possible to implement a switch which would check for duplicate parameters on the command line vs. .def file, give precedence to the command line and run the job like that? That way we would not break the existing scheme, which other people may have already grown accustomed too. Other suggestions are welcome too. Cheers, Carsten

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conversion from h3 to r3 with phenix apps
by Green, Todd 14 Aug '07

14 Aug '07

Hello all, I have what i believe to be a rhombohedral crystal that has an insanely large cell with the hexagonal setting: 533.026 533.026 652.887 90.000 90.000 120.000 and a modestly large cell comparatively with the rhombohedral setting: 377 377 377 90 90 90 I should be able to easily reindex to the smaller cell in scalepack but for some reason i'm not getting it to work correctly. Rather than struggle further on a friday afternoon, i figured that i'd give a phenix app a try. i assume xtriage can do this, can someone point me in the correct direction? thanks in advance- Todd

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refinement questions
by Sudharsan Sridharan 10 Aug '07

10 Aug '07

Hi all, I'm starting to refine a structure using phenix.refine. Almost all my model residues have been built starting from a Sharp map. I've been trying phenix.refine with and without SA and getting bond angle rmsds of 1.0 -1.1 (2.5 A data, using mlhl targets; example below) (yet to add water and also trying water picking in phenix.refine). I'm wondering if this sounds low (I have read discussions on bond and angle rmsds). More importantly I'd like to know how to work with different parameters (weights etc) during refinement in phenix. Could you please point to what params are safe to manipulate. Thanks, Sid. REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.3637 r_free = 0.4003 bonds = 0.010 angles = 1.175 REMARK Final: r_work = 0.2607 r_free = 0.3236 bonds = 0.007 angles = 1.017 REMARK ************************************************************************

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Position for PSI Knowledgebase development
by Paul Adams 08 Aug '07

08 Aug '07

======================================================================= Lawrence Berkeley National Laboratory Software Developer II ======================================================================= Software Developer II Job ID: 20930 Division: Physical Biosciences Date Opened: 8/7/2007 Summary This position will be part of the Computational Crystallography Initiative at Lawrence Berkeley Lab and will be responsible for developing a web site to disseminate information about the Technologies developed by the NIH Protein Structure Initiative (PSI). This program funds the majority of structural genomics efforts within the US and is responsible for the development of many new technologies that are useful to macromolecular crystallographers. This technology resource is part of the larger PSI Knowledge Base that will provide an information portal for the scientific community. Duties Essential: Under general direction of the Principal Investigator: Develop and maintain web site documenting PSI developed technologies. Interact with PSI researchers to collect information about new technologies. Create a relational database to store crystallographic data. Install and maintain SVN repositories for the PSI community. Marginal: Perform routine analysis of crystallographic data. Maintain web site computing hardware and software. Other duties as assigned. Qualifications Essential: Experience with writing and maintaining HTML web pages. Knowledge of standard programming methods, and Python in a UNIX environment. Strong analytical and organizational skills. Ability to handle multiple tasks in parallel. Excellent interpersonal skills for working in a diverse team environment, ability to interact effectively with other scientists, and to address their needs in an effective and timely manner. Marginal: B.S. Degree or higher in biophysics, computer science, chemistry, electrical engineering, physics or related field preferred or equivalent experience, with demonstrated programming experience. Experience maintaining computing hardware and software. Experience with analysis of crystallographic data. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20930. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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ncs restraints weight
by Daniele de Sanctis 06 Aug '07

06 Aug '07

Dear all, i'm refining a low resolution structure (3.2A) with four molecules in the asymmetric unit. I saw that phenix.refine doesn't allow constraints, so i'd like to change the restraints weight but i can't find the right keyword... thanks for your help d -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartato 127 2781-901 Oeiras Portugal

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Re: [phenixbb] set_biso_to_wilson_b gone?
by Pavel Afonine 06 Aug '07

06 Aug '07

Hi Luca, > I've just noticed that in the last version of PHENIX (1.3b-d7) this is > not recognised anymore: > > refinement.modify_start_model.adp.set_biso_to_wilson_b = true > > is this intentional? I'm afraid, yes. There are some technical reasons for this. You still have at least two ways of doing this: 1) When running phenix.refine : % phenix.refine data.mtz model.pdb modify_start_model.adp.set_b_iso=xxx where xxx is Wilson B values (that you may get from previous phenix.refine runs; phenix.refine reports it). 2) We recently added a tool for PDB file(s) manipulations. Currently it is very simple but will grow based on needs and user's requests. For example, it can read in a model and for selected or all atoms: - modify ADP (randomize, shift, set to a value, scale, convert to/from iso(aniso)tropic); - modify sites (shake, apply rotation / translation); - modify occupancies; - remove selected atoms; - write out a PDB file with modified model. To get started type: phenix.pdbtools -h I'm attaching a copy of a quick manual for phenix.pdbtools (it will be a part of new updated PHENIX documentation). Pavel.

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Re: [phenixbb] Problematic dataset
by Peter Zwart 06 Aug '07

06 Aug '07

Hi Lucas, Your P21 just looks twinned. Have a look at the last section of the xtriage output: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 1.915 - <F>^2/<F^2> : 0.821 - <|E^2-1|> : 0.677 - <|L|>, <L^2>: 0.442, 0.267 Multivariate Z score L-test: 3.623 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | h,-k,-h-l | PM | 0.090 | 0.406 | 0.417 | 0.370 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 6.379 (correpsonding p value : 6.273e-01) The largest off-origin peak in the Patterson function is 6.38% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are twin laws possible given the crystal symmetry, twinning could be the reason for the departure of the intensity statistics from normality. It might be worthwhile carrying out refinement with a twin specific target function. ------------------------------------------------------------------------------- You might have NCS parallel to the twin axis. If you run mmtbx.xtwin_map_utils on your P21 data, you get a mtzfile called obs_and_calc.mtz push that through xtriage (make sure to specify labels for observed and calculated data) to get the RvsR statistic. When you do that, please also provide the keyword 'perform=True' on the xtriage command line for my pleasure and send me the resulting log file. I guess the twin refinement will push the r values down a bit. Note that for futurte reference, xtriage produces a logfile as well, usually named logfile.log unless you ask it to be a different name. logfile.log contains some ccp4 style graphs you can view with loggraph (such as the L, NZ, Britton and H curves). If the above is too cryptic and you need more info, please let me know. HTH Peter Lucas Bleicher wrote: > Hi, Peter! > > I am sending the xtriage output for both space groups. > > So, the correct approach would be to use the MTZ > processed in P21 with the twin law from the xtriage > output from this MTZ file? > > Thanks in advance, > Lucas > > > Alertas do Yahoo! Mail em seu celular. Saiba mais em http://br.mobile.yahoo.com/mailalertas/ > ------------------------------------------------------------------------ > > ############################################################# > ## mmtbx.xtriage ## > ## ## > ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## > ## ## > ############################################################# > Date 2007-07-31 Time 16:43:49 BRT -0300 > > > ##-------------------------------------------## > ## WARNING: ## > ## Number of residues unspecified ## > ##-------------------------------------------## > > > Effective parameters: > scaling.input { > parameters { > asu_contents { > n_residues = None > n_bases = None > n_copies_per_asu = None > } > misc_twin_parameters { > missing_symmetry { > tanh_location = 0.08 > tanh_slope = 50 > } > twinning_with_ncs { > perform_analyses = False > n_bins = 7 > } > twin_test_cuts { > low_resolution = 10 > high_resolution = None > isigi_cut = 3 > completeness_cut = 0.85 > } > } > reporting { > verbose = 1 > log = "logfile.log" > ccp4_style_graphs = True > } > } > xray_data { > file_name = "LamNatP1High_scala1.mtz" > obs_labels = "MEAN_lnls,SIGIMEAN_lnls" > calc_labels = None > unit_cell = 52.16379929 64.59190369 108.2256012 89.99259949 89.99089813 \ > 66.10500336 > space_group = "P 1" > high_resolution = None > low_resolution = None > } > } > <scitbx_array_family_flex_ext.double object at 0xb5e96dac> > > > Symmetry, cell and reflection file content summary > > Miller array info: LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls > Observation type: xray.amplitude > Type of data: double, size=94082 > Type of sigmas: double, size=94082 > Number of Miller indices: 94082 > Anomalous flag: False > Unit cell: (52.1638, 64.5919, 108.226, 89.9926, 89.9909, 66.105) > Space group: P 1 (No. 1) > Systematic absences: 0 > Centric reflections: 0 > Resolution range: 26.0819 1.85 > Completeness in resolution range: 0.854134 > Completeness with d_max=infinity: 0.853839 > > ##----------------------------------------------------## > ## Basic statistics ## > ##----------------------------------------------------## > > > Matthews coefficient and Solvent content statistics > > Number of residues unknown, assuming 50% solvent content > > ---------------------------------------------------------------- > | Best guess : 1220 residues in the asu | > ---------------------------------------------------------------- > > > Completeness and data strength analyses > > The following table lists the completeness in various resolution > ranges, after applying a I/sigI cut. Miller indices for which > individual I/sigI values are larger than the value specified in > the top row of the table, are retained, while other intensities > are discarded. The resulting completeness profiles are an indication > of the strength of the data. > > ---------------------------------------------------------------------------------------- > | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | > ---------------------------------------------------------------------------------------- > | 26.08 - 4.55 | 97.0% | 96.3% | 95.5% | 93.5% | 87.3% | 80.3% | > | 4.55 - 3.62 | 96.5% | 96.1% | 95.4% | 93.8% | 87.8% | 81.2% | > | 3.62 - 3.16 | 95.7% | 94.5% | 93.2% | 89.4% | 78.1% | 66.3% | > | 3.16 - 2.87 | 93.1% | 90.7% | 87.1% | 79.1% | 60.8% | 44.5% | > | 2.87 - 2.67 | 88.4% | 84.0% | 78.5% | 66.7% | 44.0% | 27.9% | > | 2.67 - 2.51 | 85.5% | 78.6% | 71.1% | 57.7% | 32.6% | 17.9% | > | 2.51 - 2.38 | 82.4% | 74.1% | 65.3% | 49.3% | 24.8% | 12.2% | > | 2.38 - 2.28 | 81.6% | 72.3% | 62.4% | 46.0% | 20.4% | 9.0% | > | 2.28 - 2.19 | 78.5% | 67.6% | 55.1% | 37.2% | 14.8% | 5.7% | > | 2.19 - 2.12 | 75.5% | 61.9% | 49.0% | 30.7% | 9.9% | 3.5% | > | 2.12 - 2.05 | 72.1% | 55.6% | 41.8% | 23.7% | 6.3% | 1.9% | > | 2.05 - 1.99 | 68.6% | 50.2% | 35.8% | 17.9% | 4.1% | 1.0% | > | 1.99 - 1.94 | 63.2% | 42.9% | 28.5% | 13.7% | 3.1% | 0.5% | > | 1.94 - 1.89 | 56.6% | 36.7% | 23.2% | 10.4% | 1.7% | 0.3% | > ---------------------------------------------------------------------------------------- > > The completeness of data for which I/sig(I)>3.00, exceeds 85% for > for resolution ranges lower than 2.87A. > The data is cut at this resolution for the potential twin tests > and intensity statistics. > > > Maximum likelihood isotropic Wilson scaling > ML estimate of overall B value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > 15.59 A**(-2) > Estimated -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > -2.45 > > > Maximum likelihood anisotropic Wilson scaling > ML estimate of overall B_cart value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > 15.61, 1.39, -1.33 > 11.40, 0.27 > 21.10 > Equivalent representation as U_cif: > 0.18, -0.04, -0.02 > 0.14, 0.00 > 0.27 > > ML estimate of -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > -2.45 > Correcting for anisotropy in the data > > Some basic intensity statistics follow. > > > > Low resolution completeness analyses > > The following table shows the completeness > of the data to 5 Angstrom. > unused: - 26.0822 [ 0/38 ] 0.000 > bin 1: 26.0822 - 10.5555 [528/541] 0.976 > bin 2: 10.5555 - 8.4726 [551/564] 0.977 > bin 3: 8.4726 - 7.4299 [530/547] 0.969 > bin 4: 7.4299 - 6.7636 [568/582] 0.976 > bin 5: 6.7636 - 6.2860 [525/540] 0.972 > bin 6: 6.2860 - 5.9200 [547/559] 0.979 > bin 7: 5.9200 - 5.6266 [530/546] 0.971 > bin 8: 5.6266 - 5.3839 [519/532] 0.976 > bin 9: 5.3839 - 5.1783 [568/584] 0.973 > bin 10: 5.1783 - 5.0009 [516/532] 0.970 > unused: 5.0009 - [ 0/0 ] > > > > Mean intensity analyses > Analyses of the mean intensity. > Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. > The following resolution shells are worrisome: > ------------------------------------------------ > | d_spacing | z_score | compl. | <Iobs>/<Iexp> | > ------------------------------------------------ > | 9.993 | 7.15 | 0.97 | 0.426 | > | 8.448 | 7.29 | 0.98 | 0.559 | > | 7.451 | 6.09 | 0.97 | 0.676 | > | 4.303 | 4.64 | 0.97 | 1.223 | > | 3.410 | 4.52 | 0.96 | 1.176 | > | 3.333 | 6.63 | 0.96 | 1.262 | > | 3.261 | 5.36 | 0.96 | 1.205 | > | 3.194 | 5.48 | 0.96 | 1.203 | > | 3.071 | 4.87 | 0.94 | 1.183 | > | 2.962 | 6.43 | 0.94 | 1.245 | > | 2.911 | 4.61 | 0.93 | 1.160 | > | 2.454 | 4.96 | 0.87 | 0.872 | > | 2.425 | 6.89 | 0.87 | 0.825 | > | 2.397 | 4.68 | 0.87 | 0.873 | > | 2.182 | 6.79 | 0.84 | 0.830 | > | 2.142 | 5.54 | 0.84 | 0.856 | > | 1.870 | 5.46 | 0.60 | 1.205 | > | 1.857 | 11.65 | 0.54 | 1.570 | > ------------------------------------------------ > > Possible reasons for the presence of the reported > unexpected low or elevated mean intensity in > a given resolution bin are : > - missing overloaded or weak reflections > - suboptimal data processing > - satelite (ice) crystals > - NCS > - translational pseudo symmetry (detected elsewhere) > - outliers (detected elsewhere) > - ice rings (detected elsewhere) > - other problems > Note that the presence of abnormalities > in a certain region of reciprocal space might > confuse the data validation algorithm throughout > a large region of reciprocal space, even though > the data is acceptable in those areas. > > > Possible outliers > Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 > > Acentric reflections: > > ----------------------------------------------------------------- > | d_space | H K L | |E| | p(wilson) | p(extreme) | > ----------------------------------------------------------------- > | 2.114 | -18, -9, 35 | 3.79 | 5.57e-07 | 5.08e-02 | > | 3.066 | -16, -8, 12 | 3.93 | 1.90e-07 | 1.77e-02 | > | 3.066 | 16, 8, 12 | 3.95 | 1.69e-07 | 1.57e-02 | > | 2.115 | 18, 9, 35 | 3.79 | 5.65e-07 | 5.15e-02 | > ----------------------------------------------------------------- > > p(wilson) : 1-(1-exp[-|E|^2]) > p(extreme) : 1-(1-exp[-|E|^2])^(n_acentrics) > p(wilson) is the probability that an E-value of the specified > value would be observed when it would selected at random from > the given data set. > p(extreme) is the probability that the largest |E| value is > larger or equal then the observed largest |E| value. > > Both measures can be used for outlier detection. p(extreme) > takes into account the size of the dataset. > > > Centric reflections: > > None > > > Ice ring related problems > > The following statistics were obtained from ice-ring > insensitive resolution ranges > mean bin z_score : 3.46 > ( rms deviation : 1.89 ) > mean bin completeness : 0.89 > ( rms deviation : 0.09 ) > > The following table shows the z-scores > and completeness in ice-ring sensitive areas. > Large z-scores and high completeness in these > resolution ranges might be a reason to re-assess > your data processsing if ice rings were present. > > ------------------------------------------------ > | d_spacing | z_score | compl. | Rel. Ice int. | > ------------------------------------------------ > | 3.897 | 0.51 | 0.97 | 1.000 | > | 3.669 | 1.87 | 0.97 | 0.750 | > | 3.441 | 4.52 | 0.96 | 0.530 | > | 2.671 | 3.84 | 0.89 | 0.170 | > | 2.249 | 3.61 | 0.87 | 0.390 | > | 2.072 | 3.23 | 0.82 | 0.300 | > | 1.948 | 0.62 | 0.76 | 0.040 | > | 1.918 | 0.44 | 0.73 | 0.180 | > | 1.883 | 5.46 | 0.60 | 0.030 | > ------------------------------------------------ > > Abnormalities in mean intensity or completeness at > resolution ranges with a relative ice ring intensity > lower then 0.10 will be ignored. > > No ice ring related problems detected. > If ice rings were present, the data does not look > worse at ice ring related d_spacings as compared > to the rest of the data set > > > > > Basic analyses completed > > ##----------------------------------------------------## > ## Twinning Analyses ## > ##----------------------------------------------------## > > > > Using data between 10.00 to 2.87 Angstrom. > > Determining possible twin laws. > > The following twin laws have been found: > > --------------------------------------------------------------------------------- > | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | > --------------------------------------------------------------------------------- > | PM | 2-fold | 0.009 | 0.010 | 0.000 | -h,-k,l | > | PM | 2-fold | 0.090 | 0.079 | 0.001 | -h,-h+k,-l | > | PM | 2-fold | 0.099 | 0.080 | 0.001 | h,h-k,-l | > --------------------------------------------------------------------------------- > M: Merohedral twin law > PM: Pseudomerohedral twin law > > 0 merohedral twin operators found > 3 pseudo-merohedral twin operators found > In total, 3 twin operator were found > > > Number of centrics : 0 > Number of acentrics : 27599 > > Largest patterson peak with length larger then 15 Angstrom > > Frac. coord. : 0.119 -0.276 -0.000 > Distance to origin : 16.337 > Height (origin=100) : 5.893 > p_value(height) : 7.365e-01 > > The reported p_value has the following meaning: > The probability that a peak of the specified height > or larger is found in a Patterson function of a > macro molecule that does not have any translational > pseudo symmetry is equal to 7.365e-01 > p_values smaller then 0.05 might indicate > weak translation pseudo symmetry, or the self vector of > a large anomalous scatterer such as Hg, whereas values > smaller then 1e-3 are a very strong indication for > the presence of translational pseudo symmetry. > > > > Wilson ratio and moments > > Acentric reflections > <I^2>/<I>^2 :1.932 (untwinned: 2.000; perfect twin 1.500) > <F>^2/<F^2> :0.820 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.678 (untwinned: 0.736; perfect twin 0.541) > > > > NZ test (0<=z<1) to detect twinning and possible translational NCS > > > ----------------------------------------------- > | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | > ----------------------------------------------- > | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | > | 0.1 | 0.046 | 0.095 | 0.000 | 0.248 | > | 0.2 | 0.127 | 0.181 | 0.000 | 0.345 | > | 0.3 | 0.210 | 0.259 | 0.000 | 0.419 | > | 0.4 | 0.287 | 0.330 | 0.000 | 0.474 | > | 0.5 | 0.361 | 0.394 | 0.000 | 0.520 | > | 0.6 | 0.427 | 0.451 | 0.000 | 0.561 | > | 0.7 | 0.486 | 0.503 | 0.000 | 0.597 | > | 0.8 | 0.544 | 0.551 | 0.000 | 0.629 | > | 0.9 | 0.597 | 0.593 | 0.000 | 0.657 | > | 1.0 | 0.643 | 0.632 | 0.000 | 0.683 | > ----------------------------------------------- > | Maximum deviation acentric : 0.055 | > | Maximum deviation centric : 0.683 | > | | > | <NZ(obs)-NZ(twinned)>_acentric : -0.024 | > | <NZ(obs)-NZ(twinned)>_centric : -0.467 | > ----------------------------------------------- > > > L test for acentric data > > using difference vectors (dh,dk,dl) of the form: > (2hp,2kp,2lp) > where hp, kp, and lp are random signed integers such that > 2 <= |dh| + |dk| + |dl| <= 8 > > Mean |L| :0.441 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.267 (untwinned: 0.333; perfect twin: 0.200) > > The distribution of |L| values indicates a twin fraction of > 0.08. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > > > --------------------------------------------- > Analysing possible twin law : -h,-k,l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.053 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.005 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.447 > Estimation of twin fraction via cum. dist. of H: 0.449 > > > > Britton analyses > > Extrapolation performed on 0.47 < alpha < 0.495 > Estimated twin fraction: 0.442 > Correlation: 0.9953 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.054 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.004 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.415 > > > --------------------------------------------- > Analysing possible twin law : -h,-h+k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.093 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.015 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.407 > Estimation of twin fraction via cum. dist. of H: 0.407 > > > > Britton analyses > > Extrapolation performed on 0.44 < alpha < 0.495 > Estimated twin fraction: 0.399 > Correlation: 0.9959 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.093 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.011 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.361 > > > --------------------------------------------- > Analysing possible twin law : h,h-k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.085 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.013 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.415 > Estimation of twin fraction via cum. dist. of H: 0.417 > > > > Britton analyses > > Extrapolation performed on 0.46 < alpha < 0.495 > Estimated twin fraction: 0.411 > Correlation: 0.9961 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.086 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.009 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.350 > > > > Exploring higher metric symmetry > > The point group of data as dictated by the space group is P 1 > the point group in the niggli setting is P 1 > The point group of the lattice is Hall: C 2 2 (x+y,2*y,z) > A summary of R values for various possible point groups follow. > > ----------------------------------------------------------------------------------------------- > | Point group | mean R_used | max R_used | mean R_unused | min R_unused | choice | > ----------------------------------------------------------------------------------------------- > | Hall: C 2y (x-y,2*x,z) | 0.086 | 0.086 | 0.054 | 0.054 | | > | P 1 | None | None | 0.070 | 0.054 | | > | Hall: C 2y (x+y,2*y,z) | 0.093 | 0.093 | 0.054 | 0.054 | | > | Hall: C 2 2 (x+y,2*y,z) | 0.070 | 0.086 | None | None | | > | P 1 1 2 | 0.054 | 0.054 | 0.093 | 0.093 | <--- | > ----------------------------------------------------------------------------------------------- > > R_used: mean and maximum R value for symmetry operators *used* in this point group > R_unused: mean and minimum R value for symmetry operators *not used* in this point group > The likely point group of the data is: P 1 1 2 > > Possible space groups in this point groups are: > Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90) > Space group: P 1 2 1 (No. 3) > > Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90) > Space group: P 1 21 1 (No. 4) > > Note that this analyses does not take into account the effects of twinning. > If the data is (allmost) perfectly twinned, the symmetry will appear to be > higher than it actually is. > > > > > > ------------------------------------------------------------------------------- > Twinning and intensity statistics summary (acentric data): > > Statistics independent of twin laws > - <I^2>/<I>^2 : 1.932 > - <F>^2/<F^2> : 0.820 > - <|E^2-1|> : 0.678 > - <|L|>, <L^2>: 0.441, 0.267 > Multivariate Z score L-test: 3.807 > The multivariate Z score is a quality measure of the given > spread in intensities. Good to reasonable data is expected > to have a Z score lower than 3.5. > Large values can indicate twinning, but small values do not > neccesarily exclude it. > > > Statistics depending on twin laws > ------------------------------------------------------------------- > | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | > ------------------------------------------------------------------- > | -h,-k,l | PM | 0.054 | 0.442 | 0.449 | 0.415 | > | -h,-h+k,-l | PM | 0.093 | 0.399 | 0.407 | 0.361 | > | h,h-k,-l | PM | 0.086 | 0.411 | 0.417 | 0.350 | > ------------------------------------------------------------------- > > Patterson analyses > - Largest peak height : 5.893 > (correpsonding p value : 7.365e-01) > > > The largest off-origin peak in the Patterson function is 5.89% of the > height of the origin peak. No significant pseudotranslation is detected. > > The results of the L-test indicate that the intensity statistics > are significantly different then is expected from good to reasonable, > untwinned data. > As there are twin laws possible given the crystal symmetry, twinning could > be the reason for the departure of the intensity statistics from normality. > It might be worthwhile carrying refinement with a twin specific target function. > > Note that the symmetry of the intensities suggest that the assumed space group > is too low. As twinning is however suspected, it is not immediuatly clear if this > is the case. Carefull reprocessing and (twin)refinement for all cases might resolve > this question. > > -------------------------------------------------------------------------------

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R, Rfree, and wxu_scale
by Jianghai Zhu 05 Aug '07

05 Aug '07

Hi, Just finished a round of refinement. Rfree went up about 1% and R went down a bit. I am wondering what happened here. Also Rfree always went down after TLS refinement but always went up a lot more after the individual ADP refinement. Is there anything I can do here? Should I use weaker B restraints? I tried to assign a wxu_scale value. But phenix.refine automatically adjust it to 1.81 every time. ------------------------------------------------------------------------ R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3982 0.5701 6.156859e+00 6.238509e+00 1_bss: 0.2008 0.2494 5.949117e+00 6.088855e+00 1_xyz: 0.2030 0.2497 5.953829e+00 6.091696e+00 1_adp: 0.1998 0.2559 5.952833e+00 6.099340e+00 2_bss: 0.1996 0.2557 5.952517e+00 6.099196e+00 2_xyz: 0.1984 0.2576 5.953246e+00 6.104085e+00 2_adp: 0.1974 0.2578 5.950434e+00 6.102336e+00 3_bss: 0.1972 0.2574 5.950333e+00 6.102222e+00 3_xyz: 0.1997 0.2576 5.956524e+00 6.103647e+00 3_adp: 0.1987 0.2590 5.955554e+00 6.104434e+00 3_bss: 0.1986 0.2588 5.955445e+00 6.104227e+00 ------------------------------------------------------------------------ Weights for target T = Exray * wxc * wxc_scale + Echem * wc and angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites) stage wxc wxu wxc_sc wxu_sc /_gxc,gc /_gxu,gu 0 : 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_bss: 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_xyz: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 1_adp: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_bss: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_xyz: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 2_adp: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_bss: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_xyz: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_adp: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_bss: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 ------------------------------------------------------------------------ Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Postdoctoral Position for PHENIX development
by Paul D. Adams 03 Aug '07

03 Aug '07

======================================================================= Lawrence Berkeley National Laboratory Computational Postdoctoral Fellow ======================================================================= Computational Postdoctoral Fellow Job ID: 20907 Division: Physical Biosciences Date Opened: 8/2/2007 Summary We are seeking an intelligent, motivated scientist to develop graphical tools for the PHENIX software system. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities will include development and implementation of graphical interfaces, user workflow tools, and mechanisms for data tracking and storage. Duties Essential - Primary duties and responsibilities will include development and implementation of computational algorithms for structure determination using X-ray crystallography. Develop graphic interfaces to components of the PHENIX software system. Create interfaces between PHENIX and other software packages such as Coot. Implement software code for capturing and tracking data and other information as it is created by the PHENIX software. This position requires interaction with P.I.s, postdocs, Scientists and external collaborators involved in the PHENIX project. Publication of research results in scientific journals and presentation of results at scientific meetings. Marginal - Actively participate in group meetings. Assume shared responsibility for maintenance of computational equipment with other group members. Qualifications Essential - Ph.D. within the last three years in computational crystallography or a related field. Demonstrated experience with graphical interface development. First-author publications in macromolecular crystallography or closely related field. Familiarity with software development tools such as C++, C or Fortran programming languages and scripting languages such as Python or Perl. Strong programming skills. Solid interpersonal skills and the ability to work in a team environment are critical. Marginal - Experience with the practical aspects of protein crystallography: protein production, crystallization and structure solution. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about PHENIX visit: http://www.phenix-online.org/ For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20907. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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