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Re: [phenixbb] Problematic dataset
by Peter Zwart 05 Aug '07

05 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. > > -------------------------------------------------------------------------------

1 0

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 +++++++++++++++++++++++++++++++

3 9

Postdoctoral Position for PHENIX development
by Paul D. Adams 02 Aug '07

02 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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estimated coordinate error
by Jianghai Zhu 01 Aug '07

01 Aug '07

Hi, I am refining a 2.6 A structure using both phenix.refine and refmac5. Both programs give me similar R and Rfree values. But the estimated coordinate errors are quite different. From phenix.refine: maximum likelihood estimate for coordinate error: 0.42 A From refmac5: estimated overall coordinate error: ESU based on R value: 0.427 A ESU based on Free R value: 0.293 A ESU based on maximum likelihood: 0.239 A I am wondering why they are different. 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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General Question !!!
by john kryst 01 Aug '07

01 Aug '07

Hi all !! Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement. regards John

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AutoSol problem
by Ben Eisenbraun 31 Jul '07

31 Jul '07

Hi- One of my users is running the Linux 64-bit version of Phenix-1.3b and they are getting the following message at the end of their logfile: ************************************************************ Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked ************************************************************ The solve part of Phenix looks like it built correctly: $ ls -l phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/ -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment_pair -rwxr-xr-x 1 sbgrid sbgrid 3483160 Jun 27 16:55 resolve -rwxr-xr-x 1 sbgrid sbgrid 3483576 Jun 27 16:55 resolve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 3483256 Jun 27 16:55 resolve_giant -rwxr-xr-x 1 sbgrid sbgrid 3482968 Jun 27 16:55 resolve_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_giant -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_huge -rwxr-xr-x 1 sbgrid sbgrid 1547840 Jun 27 16:55 segment_library -rwxr-xr-x 1 sbgrid sbgrid 1575648 Jun 27 16:55 side_chains -rwxr-xr-x 1 sbgrid sbgrid 1566208 Jun 27 16:55 side_chains_update -rwxr-xr-x 1 sbgrid sbgrid 5327984 Jun 27 16:55 solve -rwxr-xr-x 1 sbgrid sbgrid 11331152 Jun 27 16:55 solve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 6529136 Jun 27 16:55 solve_giant -rwxr-xr-x 1 sbgrid sbgrid 7729424 Jun 27 16:55 solve_huge -rwxr-xr-x 1 sbgrid sbgrid 11393392 Jun 27 16:55 solve_mx $ file phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0, statically linked, for GNU/Linux 2.4.0, stripped We do have a standalone Solve install with its corresponding SOLVEDIR, etc, environment variables. Could that be confusing Phenix? I have the complete logfile, but it's rather long. If it would help, it can be made available. Any ideas on what I should do to troubleshoot this? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/

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TEST - please ignore
by Luca Jovine 31 Jul '07

31 Jul '07

Sorry, just re-testing whether my e-mails to phenixbb are still vanishing into nowhere...

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A question about AutoBuild
by Marcelo Carlos Sousa 30 Jul '07

30 Jul '07

We have solved (in part) a structure by Molecular Replacement. The protein is a homodimer with 360 amino acids per chain (one dimmer per asu). The model was pretty good for the last 220 amino acids or so but appears to be wrong for the first 140 so I deleted them and refined using phenix to an R free of ~ 0.38. As I was about to start model building in O I thought I would give the phenix autobuild a try. The resolution is 2.5 Å and the map shows buildable features for the missing domain. I ran the autobuild wizard with RESOLVE building “in- place” to extend the current model. However the program seemed unable to add fragments of secondary structure (even as alanines) to the model. The question is: is the building “in-place” restricted to “growing” the current model from the ends? Marcelo

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part II. A question about autobuild
by Marcelo Carlos Sousa 30 Jul '07

30 Jul '07

I also noticed that water molecules are assigned to the buildable parts of the map.

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R-factor problem !!!
by john kryst 30 Jul '07

30 Jul '07

Hi all !! I am using phenix.refine to refine my 3.2 A structure. Also i use xtal_pdbsubmission utility in CNS to generate pdb file which is submission ready format. Please note no refinement in CNS only formating. Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ?? As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us. Thanks in advance for your inputs regards John

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