July 2014 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

6 8

Refinement with new mtz.file
by Aleksandar Bijelic 14 Jul '15

14 Jul '15

Dear CCP4 user and experts, I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24 (with good geometry according to Ramachandran, Beta Outliers, etc.) .... Everything seems to be ok (especially in relation to the resolution) .... because the mtz.file I used was quite old and I cannot find my xscale.hkl file, I processed the data set again (this time with optimizng and polishing) and received a "better" file according to almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I used this new mtz.file and put it in my last refinement step (the refinement which led to the above mentioned Rfree = 0.24). Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up with 0.20 and 0.22, respectively. So I wanted to know if this is usual? I was expecting my data to become slightlly better but what is irritating me is the starting R-values of the refinement and that it get worse during refinement. Maybe I did something wrong? Is it reasonable to replace the mtz.file with a new one in the last refinement step or should I start the refinement from the scratch? In the sake of completeness, I deleted the header of the used pdb.file because of the R-flag error which occurs, since Phenix reconizes that the pdb.file was already used with other Rflags. Sorry, but I am still a beginner in this field, so I would be very grateful if somebody could explain me this situation and my mistake and if I need to start refinement from the beginning. Thank you in advance! Best Regards. Aleksandar -- ------------------------------------------- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 A-1090 Wien Tel: +43 1 4277 52536 e-Mail: aleksandar.bijelic(a)univie.ac.at --------------------------------------------

7 10

how to refine everything except n residues in phenix.refine?
by Murpholino Peligro 22 Oct '14

22 Oct '14

Hi everybody! Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups. Can I tell phenix.refine not to move only those two residues? It should be something like the following lines in the eff file? sites { individual = None torsion_angles = None rigid_body = None remove_selection=resid 45 remove_selection=resid 68 } Thank you very much

4 8

Two ions at same position
by Eric Girard 08 Aug '14

08 Aug '14

Dear phenixbb members, I am refining a structure that contains Ca2+ atoms. The structure was determined in presence of lanthanide ions. Thus, the resulting density clearly indicates that a part of each Ca2+ sites is substituted with Eu3+ (let's say 75% Ca2+ and 25% Eu3+ per sites). How can I deal with such situation? Indeed phenix.refine complains when I try to put a Ca2+ ion and a Eu3+ one with the same coordinates (and with the occupancies mentionned above) and stop. Thanks for your help. Eric. -- **************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale UMR 5075 CEA-CNRS-UJF-PSB 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 Phone: +33 (0)4 57 42 86 45 Fax: +33 (0)4 76 50 18 90 Web site: http://www.ibs.fr/ *****************************************************************

3 4

command line
by PC 08 Aug '14

08 Aug '14

3 3

Two ions at same position
by Eric Girard 04 Aug '14

04 Aug '14

Dear phenixbb members, I am refining a structure that contains Ca2+ atoms. The structure was determined in presence of lanthanide ions. Thus, the resulting density clearly indicates that a part of each Ca2+ sites is substituted with Eu3+ (let's say 75% Ca2+ and 25% Eu3+ per sites). How can I deal with such situation? Indeed phenix.refine complains when I try to put a Ca2+ ion and a Eu3+ one with the same coordinates (and with the occupancies mentionned above) and stop. Thanks for your help. Eric. -- **************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale UMR 5075 CEA-CNRS-UJF-PSB 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 Phone: +33 (0)4 57 42 86 45 Fax: +33 (0)4 76 50 18 90 Web site: http://www.ibs.fr/ *****************************************************************

5 6

lower Rfree in phenix.maps compared to phenix.refine and phenix.reciprocal_space_arrays
by Gregers Rom Andersen 02 Aug '14

02 Aug '14

Dear bb I have encountered a quite significant difference between Rfree reported by phenix.maps, refine and reciprocal_space_arrays. I have used default values in the GUI, and don't find differences in reflections statistics reported in the phenix.maps log that could explain the difference. I have another example also, but with a smaller difference between phenix.maps and phenix.refine. Both are quite large structures with maximum resolution between 3.5 and 4. Any explanation? phenix.maps ------------------------------------------------------------------------------- Bulk solvent correction and anisotropic scaling: |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A | | | | x-ray target function (ml) for work reflections: 6.433959 | |-----------------------------------------------------------------------------| phenix.reciprocal_space_arrays |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A | | | | x-ray target function (ml) for work reflections: 6.492710 | |-----------------------------------------------------------------------------| phenix.refine, strategy=none 1 macrocycle |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A | | | | x-ray target function (ml) for work reflections: 6.492702 | |-----------------------------------------------------------------------------| gregers Professor Gregers Rom Andersen Department of Molecular Biology and Genetics Aarhus University Gustav Wiedsvej 10C DK8000 Aarhus C phone +45 871 55507 fax +45 861 23178 email gra(a)mb.au.dk -------------extract of log files-------- phenix.maps log Parameters to compute maps:: maps { input { pdb_file_name = "/u/gra/myproject/juli2014/mave/ref_01.pdb" reflection_data { file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz" labels = "FP,SIGFP" high_resolution = None low_resolution = None outliers_rejection = True french_wilson_scale = True french_wilson { max_bins = 60 min_bin_size = 40 } sigma_fobs_rejection_criterion = None sigma_iobs_rejection_criterion = None r_free_flags { file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz" label = "R-free-flags43" test_flag_value = 1 ignore_r_free_flags = False } } } =============================== Reflection data =============================== F-obs: /u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=22776 Type of sigmas: double, size=22776 Number of Miller indices: 22776 Anomalous flag: False Unit cell: (168.063, 154.031, 78.988, 90, 90, 90) Space group: P 21 21 2 (No. 18) Systematic absences: 0 Centric reflections: 2864 Resolution range: 29.4462 3.67631 Completeness in resolution range: 0.992029 Completeness with d_max=infinity: 0.989401 Wavelength: 0.0000 Number of F-obs in resolution range: 22776 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 29.4462 d_min = 3.6763 R-free flags: /u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43 Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43 Observation type: None Type of data: int, size=22776 Type of sigmas: None Number of Miller indices: 22776 Anomalous flag: False Unit cell: (168.063, 154.031, 78.988, 90, 90, 90) Space group: P 21 21 2 (No. 18) Systematic absences: 0 Centric reflections: 2864 Resolution range: 29.4462 3.67631 Completeness in resolution range: 0.992029 Completeness with d_max=infinity: 0.989401 Wavelength: 0.0000 Test (R-free flags) flag value: 1 Number of work/free reflections by resolution: work free %free bin 1: 29.4471 - 7.8747 [2434/2441] 2190 244 10.0% bin 2: 7.8747 - 6.2702 [2347/2348] 2103 244 10.4% bin 3: 6.2702 - 5.4834 [2297/2300] 2076 221 9.6% bin 4: 5.4834 - 4.9847 [2284/2286] 2053 231 10.1% bin 5: 4.9847 - 4.6289 [2272/2274] 2045 227 10.0% bin 6: 4.6289 - 4.3569 [2294/2295] 2066 228 9.9% bin 7: 4.3569 - 4.1393 [2240/2241] 1994 246 11.0% bin 8: 4.1393 - 3.9595 [2254/2255] 2027 227 10.1% bin 9: 3.9595 - 3.8074 [2277/2278] 2055 222 9.7% bin 10: 3.8074 - 3.6763 [2077/2241] 1853 224 10.8% overall 20462 2314 10.2% ------------------------------------------------------------------------------- Input model file: /u/gra/myproject/juli2014/mave/ref_01.pdb ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 48 15.91 1 P 28 14.91 1 Mg 2 11.95 2 O 2498 7.97 1 N 2146 6.97 1 C 7880 5.97 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 12602 At special positions: 0 Unit cell: (168.063, 154.031, 78.988, 90, 90, 90) Space group: P 21 21 2 (No. 18) ------------------------------------------------------------------------------- Bulk solvent correction and anisotropic scaling: |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A | | | | x-ray target function (ml) for work reflections: 6.433959 | |-----------------------------------------------------------------------------| phenix.reciprocal_space_arrays Default params:: hkl_file = None pdb_file = None f_obs_label = None r_free_flags_label = None remove_f_obs_outliers = True bulk_solvent_and_scaling = True hendrickson_lattman_coefficients_label = None output_file_name = None space_group = None unit_cell = None job_title = None |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A | | | | x-ray target function (ml) for work reflections: 6.492710 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.4471 - 9.3567 0.99 1316 144 0.1750 0.1935 7.111 7.2567| | 2: 9.3567 - 7.4666 1.00 1244 147 0.1844 0.2442 6.8649 7.0955| | 3: 7.4666 - 6.5345 1.00 1243 135 0.2403 0.3183 6.6514 6.7683| | 4: 6.5345 - 5.9424 1.00 1221 136 0.2622 0.3386 6.5345 6.547| | 5: 5.9424 - 5.5195 1.00 1230 131 0.2482 0.3091 6.3934 6.5161| | 6: 5.5195 - 5.1959 1.00 1199 141 0.2741 0.2699 6.3987 6.4315| | 7: 5.1959 - 4.9370 1.00 1196 129 0.2528 0.2600 6.3987 6.4955| | 8: 4.9370 - 4.7230 1.00 1227 136 0.2747 0.3240 6.4448 6.5001| | 9: 4.7230 - 4.5418 1.00 1178 151 0.2867 0.3278 6.4205 6.5232| | 10: 4.5418 - 4.3856 1.00 1224 113 0.2871 0.2980 6.4246 6.5162| | 11: 4.3856 - 4.2489 1.00 1201 151 0.3209 0.4007 6.4221 6.5583| | 12: 4.2489 - 4.1278 1.00 1174 137 0.3552 0.3395 6.4274 6.4033| | 13: 4.1278 - 4.0194 1.00 1190 129 0.3917 0.3944 6.4059 6.366| | 14: 4.0194 - 3.9216 1.00 1184 149 0.3931 0.3915 6.3718 6.38| | 15: 3.9216 - 3.8326 1.00 1221 116 0.3952 0.3998 6.3442 6.3031| | 16: 3.8326 - 3.7512 1.00 1168 138 0.4077 0.3949 6.334 6.3252| | 17: 3.7512 - 3.6763 0.88 1040 130 0.4322 0.4220 6.3237 6.2334| |-----------------------------------------------------------------------------| ------------------------------- phenix.refine refine { strategy = individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous main { number_of_macro_cycles = 1 ============================= updating all scales ============================= start: r_work=0.3857 r_free=0.4073 n_reflections: 22776 start: r_work=0.3857 r_free=0.4073 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2758 r_free=0.3049 remove outliers: r_work=0.2758 r_free=0.3049 correct solvent mask: r_work=0.2741 r_free=0.3045 final: r_work=0.2741 r_free=0.3045 n_reflections: 22769 overall anisotropic scale matrix: V0: 0.0014,6.7700,1.3003,-6.1473,-1.1440,0.3484 V1: -0.0036,-0.0045,-0.0442,0.0324,0.0082,0.0028 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask 29.446-20.724 97.09 90 10 0.2436 1579.386 1497.822 1.000 2.341 0.338 20.553-17.465 100.00 91 10 0.2757 1238.791 1140.148 1.000 1.886 0.335 17.444-14.852 99.35 137 16 0.2182 1221.185 1176.515 1.000 1.685 0.327 14.833-12.617 98.73 210 23 0.1958 1278.964 1244.386 1.000 1.494 0.307 12.608-10.717 98.98 349 39 0.1500 1428.238 1389.811 1.000 1.395 0.300 10.715-9.108 99.84 547 62 0.1416 1410.502 1384.438 1.000 1.354 0.290 9.104-7.738 100.00 883 99 0.1789 1027.723 1002.711 1.000 1.233 0.290 7.736-6.574 99.94 1427 159 0.2385 682.594 646.245 1.000 1.076 0.290 6.573-5.586 99.88 2288 254 0.2567 515.856 486.005 1.000 0.892 0.270 5.586-4.747 99.90 3710 411 0.2654 489.477 455.553 1.000 0.818 0.220 4.746-4.033 99.95 5973 671 0.3225 441.426 390.526 1.000 0.817 0.170 4.033-3.676 96.99 4751 559 0.4048 366.235 296.284 1.000 0.848 0.170 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1939 b_overall=26.4160

2 1

Fwd: real_space_refine
by George Devaniranjan 02 Aug '14

02 Aug '14

Hi I was wondering if there is a way to restrain the omega angles of the structure being refined to its starting values while allowing the phi and psi dihedral angles to vary? I was looking at omega_esd_override_value discard_omega in phenix.real_space_refine. Thank you, George

2 3

Maximum Likelihood Method for Twinning
by Chris Fage 30 Jul '14

30 Jul '14

Hi All, Can anyone please direct me to a literature reference describing the maximum likelihood method for detection of twinning based on twin laws, as implemented in phenix.xtriage? Thank you! Best, Chris

5 7

Use of NCS in Autosol
by Nick Huang 29 Jul '14

29 Jul '14

Dear All, Does autosol use NCS averaging in its density modification? I checked the log file for an Autosol run. It seemed Autosol used NCS in heavy atom refinement but not in the density modification procedure. But I might be wrong. If this is the case, is there a way to include NCS in autosol pipeline or do I just have to run density averaging afterward? Thanks. Nick Huang Hauptman-Woodward Institute

2 1