- phenixbb - phenix-online.org

PEG dependent structural changes in crystal structure
by shivendra singh 05 Aug '14

05 Aug '14

Dear All, I have been working on a protein which initially got crystallised in condition having PEG1500 as precipitant. The space group was P21 and got solved with reasonable Rfree. Analysis of its structure showed large deviation and very distinct active site architecture along with disorderedness in one of its long loop (no density) in comparison with the expected result, based on related homologous structures. The structure does not seem to be active with one of its active site residue moved apart from other catalytic amino acids. Also the substrate entry tunnel looks distorted. The purified enzyme used for crystallisation showed optimum activity in vitro. This led us to screen it again for some other crystallisation condition and got another crystal hit in condition having PEG3350 as precipitant. Rest of the components of crystallisation cocktail were same. The data belonged to P212121 space group. The regions which were disordered or distorted in earlier case were observed to be ordered and in their expected orientation and position. The enzyme is not reported to be in different structural or functional states as observed. I am wondering how the protein from the same batch showed two distinct structural organizations in conditions with varying PEGs. What may cause it to follow such transition. Whether it has some significant functional aspect or just a result of improper crystal packing. Thanks. Shiv

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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/ *****************************************************************

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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

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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

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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

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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

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alternatives to RMSD
by Patrick. C 29 Jul '14

29 Jul '14

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real space refinement
by George Devaniranjan 28 Jul '14

28 Jul '14

Hi, I know this is going to sound blasphemous in phenix (my apology particularly to Pavel) but is there other s/w that does similar things to phenix.real_space_refine ? I used that already (works very well) but was wondering if there was anything similar out there to do a comparison. Thank you, George

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eLBOW / REEL and chirality
by L. Costenaro (IBB) 24 Jul '14

24 Jul '14

Dear all, I am making the restraints file (CIF) for a ligand with two chiral carbons, using eLBOW (AM1 QM, output: retain original chirality) from a SMILES description and obtain the following: Atom input_chirality input_smiles output_vol_sign output_R/S output_chirality_pdb C20 S C@H negative S S C37 R C@@H positive S S Although the volume_sign in the output cif file correspond to the input chiralities, the output pdb has the wrong chirality for the carbon C37: S instead of the desired R. I think the "retain original chirality" option is what I need to keep the input chirality, but apparently it doesn't. How should I proceed to get a pdb with the correct chiralities? Best regards, Lionel PS: phenix version 1.9-1692, linux X86_64 PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash (all windows close) without error message

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SFALL in CCP4 and calculate F(model) in Phenix
by PC 24 Jul '14

24 Jul '14

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Re: [phenixbb] [External] RE: phenix.ligandfit does not recognize a list of SDF file names
by Terwilliger, Thomas Charles 22 Jul '14

22 Jul '14

Hi Jason, I fixed ligandfit so that it should now be able to take your list of sdf files and run each file sequentially. Starting with tomorrow's build, you should be able test it out with this regression test: phenix_regression.wizards.test_command_line_ligands test_ligand_list Thanks for pointing out the problem! Let me know if that does not do it. All the best, Tom T On Jul 21, 2014, at 7:11 PM, Phan, Jason wrote: > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [phenixbb-bounces(a)phenix-online.org] on behalf of Phan, Jason [jason.phan(a)vanderbilt.edu] > Sent: Monday, July 21, 2014 4:32 PM > To: phenixbb(a)phenix-online.org<mailto:[email protected]> > Subject: [phenixbb] phenix.ligandfit does not recognize a list of SDF file names > > Hi All, > > I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks. > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb

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B iso average versus B wilson
by Emily Golden 21 Jul '14

21 Jul '14

Dear All, I have a 1.12 A refined structure with and average B of 11.5 but the wilson B is 6. There are a couple of highly mobile loops and water molecules in the structure that are increasing the average B. What is an acceptable difference between wilson B and average B? Thank you, Emily

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phenix.ligandfit does not recognize a list of SDF file names
by Phan, Jason 21 Jul '14

21 Jul '14

Hi All, I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks.

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CCTBX questions
by Morten Grøftehauge 21 Jul '14

21 Jul '14

Hi people, I notice that cctbx.python comes with phenix but as far as I can tell from when I run it, look at imported modules with dir(), and compare to the documentation on Sourceforge the version that comes with phenix is abridged. And possibly not the same version as the sourceforge one but they probably are the same. Will it cause any problems with Phenix if I install cctbx from sourceforge? Is it unnecessary? Second question: Is there any better documentation anywhere? I found James Stroud's wiki but that's mainly for structure factor manipulation. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Long Distant Restraints
by Bradley Hintze 18 Jul '14

18 Jul '14

Hey PHENIX, I am wondering if I can define a distant restraint longer that 3A in a custom restraint file? The conventional way of doing this is to provide : refinement.geometry_restraints.edits { C8_C1=chain C and resid 8 and name C1' D10_C1=chain D and resid 10 and name C1' bond { action = *add atom_selection_1 = $C8_C1 atom_selection_2 = $D10_C1 distance_ideal = 9.1 sigma = 0.02 slack = 0.5 } Obviously this is a distant and not bond restraint. 9.1 exceeds the allowed length of 3 for a bond. Is there a different type of restraint that allows longer distances? Thanks! -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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Refinement cycles
by George Devaniranjan 17 Jul '14

17 Jul '14

Hi, I was wondering if there is a reason for setting the default number of refinement cycles to 3 in Phenix refine? is there a number of cycles at which point it becomes unacceptable to run so many ? Thank you, George

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B factors too high for low resolution data refinement
by 李翔 15 Jul '14

15 Jul '14

Hi everyone, I am working on my low-resolution data (~6.5 A). When I was doing refinement with PHENIX, the B factors remain pretty high (~400, not sure whether it is normal for the data with such resolution.) And B factors further increased after group B factor refinement (~500). Does it mean the group B factors refinement not working or is there a way I can somehow define a limit for B-factors? (I read one previous topic a few years ago which indicates the B factor can not be controlled. Not sure whether it is available now). Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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So what is unique?
by Kenneth A. Satyshur 15 Jul '14

15 Jul '14

There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. "Unique Reflections" My definition is all the possible reflections out to the highest resolution reported not related by symmetry. Where can I find this? The .mtz contains a list of all HKL calculated to the highest resolution. Usually, we are not able to measure all these diffraction spots due to limits of the detector, mechanical limits, crystal orientation, etc. 'Total reflections' The depositions server asks for total reflections. I assume it wants only those unique reflections we were able to collect, regardless of the sigma cut off. These are called 'observed'. The total we use in refinement will be a subset of the 'unique observed' that are cut on sigma. However, some crystallographers believe that we should not cut on sigma since some of the intensities may in fact be zero. Is this a question for the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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cifs still in pdb v2
by Guenter Fritz 14 Jul '14

14 Jul '14

Dear Pavel and Nat, can you include in future phenix versions the FAD.cif, NAD.cif and data_NAI.cif / NAI.cif in pdb v3? Currently both are still pdb v2. I usually simply copy the cifs pdb v3 into the mon_lib directory , but sometimes I forget it and stumble over it. Thanks and best wishes, Guenter

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Maximum-likelihood score calculation
by Jouko Virtanen 12 Jul '14

12 Jul '14

Hi all, I would like to calculate the maximum-likelihood score given an input structure and an mtz file. How can I do that? Thanks in advance. Best regards, Jouko

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Real space implementation of DEN refinement?
by Oliver Clarke 11 Jul '14

11 Jul '14

Hi all, Just wondering whether there is any capacity to include DEN restraints in phenix.real_space_refine, e.g. as implemented in the program DireX (see ref below), or any possibility of implementing such in a future release of PHENIX? This would be very handy for refinement of models into low resolution maps (particularly EM maps). Also, on a different but related topic, does anyone have any suggestions as to how to handle model validation (local and global) at low resolution in real-space? It seems as though there is not a solid consensus on how to handle this. Many thanks, Oliver. 1. Schröder, G. F., Brünger, A. T. & Levitt, M. Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution. Structure 15, 1630–1641 (2007).)

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Twinning in data reduction and phenix.refine
by Chen Zhao 11 Jul '14

11 Jul '14

Dear all, I am now dealing with a pseudo-merohedral twin (3.2 A, P1 twinned into C2), and I have a couple of questions concerning the data reduction and refinement: 1) R-free flag in refinement a) For twin refinement, I know the reflections related by the twin law should have the same R-free flag. If I process my data in P1, and generate the R-free flag by phenix.refine using the key word xray_data.r_free_flags.use_lattice_symmetry=True, can phenix generate the R-free flags considering the 2-fold point group symmetry and deal with the twinning properly? b) I read that the R-factor could go down to around 40% in twin refinement in the presence of twinning even if the model is completely wrong. For my understanding, this could be due to the fact that the reflections are correlated by the twin law. If the R-free flags are chosen in the highest lattice symmetry, will the R-free still suffer from this problem? 2) Twin fraction In phenix.xtriage, the predicted twin fraction is about 30%. However, in phenix.refine, the twin_fraction is always between 46% to 50%. Why could this happen? 3) Data reduction I am not very clear about this point, since I just started dealing twinning. But what I am thinking is whether it is a good idea to merge the Friedel pair in the presence of twinning. Since the two twin domains have different hkl index if considering one as the reference, is the Friedel law still valid? This might be a very simple mathematical problem. I really appreciate your answers! Sincerely, Chen

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Anomalous or not?
by CPMAS Chen 10 Jul '14

10 Jul '14

Hi, Phenix Users, I recently collected data at SSRL. I used autoxds and multiscale to merge couple of datasets and hoped to see some anomalous signals. Now comes the questions. 1. if I use the default sigma(=2), then autoxds will report weak anomalous signals and leave the friedel flag off. If I lower sigma to 1.5, it will report strong anomalous signals. 2. when I used Xtriage under Phenix to check the data quality, it reported weak anomalous signal or at above 10A. 3. I used aimless (in CCP4) to merge data, it also reported weak anomalous signal. Which result should I trust? By the way, how can I view/display the ***.anamplot file, which is apparently xmgr format file, but I can not display in CCP4i. Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Re: [phenixbb] Anomalous or not?
by Ryan Spencer 10 Jul '14

10 Jul '14

The question then becomes how do you know the bromine is in the crystal? Is it covalent on the protein? Is it covalent on the ligand? How do you know if the ligand is in the structure? We have seen rapid crystal degredation with Br at its edge. Do you see the resolution significantly degrade after a few frames? I don't think it's a processing issue with xds or with phenix. Ryan -------- Original message -------- From: CPMAS Chen <cpmasmit(a)gmail.com> Date: 07/10/2014 9:52 AM (GMT-08:00) To: Ryan Spencer <rspencer(a)uci.edu> Cc: Francis Reyes <Francis.Reyes(a)colorado.edu>,phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Anomalous or not? Well, let me make this clear. 1. I am using Br anomalous signal to identify the potentially bound ligand. 2. I do shoot the crystals at 0.92A. 3. the different crystals have different resolution, but anomalous signal was weak as reported by autoxds. Charles On Thu, Jul 10, 2014 at 12:25 PM, Ryan Spencer <rspencer(a)uci.edu> wrote: So I assume you were not able to shoot the crystal at ~0.92 A at SSRL or are the crystals sensitive? If you were limited to the single wavelength beam which is around 1A you’re dealing with a really low f” of 0.5322. There have been crystals solved with Sulfur using an in-house Cu sources (takes a lot of merged sets and anomalous is stronger at certain crystal angles) which gives about the same anomalous scattering as Br. Is the bromine covalent or is it soaked ion? Alternatives – soak with potassium iodide and get a dataset from an in-house source (iodine f” 6.6 at 1.54), or at least the anomalous locations. You may get a partial model to use for replacement at that point. Did each processed dataset have the same level of anomalous signal when processed individually? Ryan From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of CPMAS Chen Sent: Thursday, July 10, 2014 8:55 AM To: Francis Reyes Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Anomalous or not? Francis, My anomalous plot for Br is more like your Cobalt 1 site less redundancy. Ryan, As my Br anomalous signals are weak, I merged signals from multiple crystals. Meanwhile I am looking into the detail about the autoxds processing as suggested by Tim. Thanks, On Thu, Jul 10, 2014 at 10:02 AM, Francis Reyes <Francis.Reyes(a)colorado.edu> wrote: In addition to Tim's comments above, using loggraph to see the anomalous CC plot from scala is a good qualitative indicator of whether you have anomalous signal.. Some data points for what reasonable plots (and their corresponding XDS SigANO's) look like: https://dl.dropboxusercontent.com/u/19558536/AnomalousCC.pdf F On Jul 10, 2014, at 9:03 AM, CPMAS Chen <cpmasmit(a)gmail.com> wrote: > > Which result should I trust? By the way, how can I view/display the ***.anamplot file, which is apparently xmgr format file, but I can not display in CCP4i. > -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ****************************************************** -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Postdoctoral Position in Membrane Protein Structural Biology
by Noinaj, Nicholas (NIH/NIDDK) [E] 07 Jul '14

07 Jul '14

Two postdoctoral positions in structural biology are available starting in August in my new laboratory within the Biological Sciences department at Purdue University. As part of the Markey Center for Structural Biology, my lab will integrate electron microscopy and X-ray crystallography with biochemical methods to study the biogenesis of beta-barrel membrane proteins in Gram-negative bacteria with a focus on eventual therapeutic development against pathogenic strains of bacteria (See Noinaj et al., Structure (in press, 2014), Nature, 501:385-390 (2013), and Nature, 483:53-58 (2012)). The Markey Center for Structural Biology at Purdue is recognized worldwide for its leadership in structural biology of viruses, membrane proteins, receptors, signaling proteins and enzymes in addition to methods development in crystallography, NMR and electron microscopy. My lab is located within the Hockmeyer Hall of Structural Biology which boasts state-of-the-art shared resources including a Titan Krios cryo-TEM, Bruker Avance-III 800 MHz NMR, Rigaku X-ray generators and detectors, and other advanced instrumentation available at the Bindley Bioscience Center, the Birck Nanotechnology Center, and the new Center for Drug Discovery. In addition, Purdue is in close proximity to the Advanced Photon Source at Argonne National Lab for convenient access to synchrotron data collection. The successful candidate(s) should be highly motivated, have strong written and communication skills, have (or expect) a recent PhD in structural biology, biophysics, biochemistry, or other related field of study and have previous experience in working with membrane proteins and/or X-ray crystallography or electron microscopy. Applicants should send a CV, names of three referees and a statement describing your interests and relevant work experience to Nicholas Noinaj at nicholas.noinaj(a)gmail.com<mailto:[email protected]>. Nicholas Noinaj Purdue University Department of Biological Sciences 333 Hockmeyer Hall 915 W State St West Lafayette, IN 47907

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Autobuiold from polyalanine model
by Chieh Yin 07 Jul '14

07 Jul '14

Dear Phenix Users, I am doing the molecular replacement to solve a membrane protein structure(transmembrane and soluble domain). The structure of the soluble domain is known, 200AAs. And there is a homology structure of transmembrane domain, 350AAs. I used the polyalanine model of the homologous model of transmembrane domain to do the first search. I got a solution with TFZ 16. Then used the partial solution to do the second search with the soluble domain as the model.I also got a solution with TFZ about 15. The density map showed I got the right solution. And the simple rigid body refinement yielded a Rfactor/Rfree 0.29/0.32. Then I used the polyalanine model and the soluble domain as the starting model to do the phenix autobuild. But it seemed that Autobuild didn't replace the alanine with the real sequence AAs. I tried to set the rebuild in place to false but I still got the same result. The Autobuild even didn't change any amino aside reside from the starting model. I hope you could figure out the problem for me. Thank you in advance! Best regards, Jie

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distinguish between metals
by Aleksandar Bijelic 01 Jul '14

01 Jul '14

Dear phenix developers and users, I wanted to ask if there is a possibility to considerably distinguish betwenn two/three metals. I crystallized an iron-binding protein (transferrin in apo form) with a Ru- and Ga-compound. I see density in the metal-binding site which should come from the Ru/Ga metal since crystallization was done with the apo-form, but nevertheless I need to prove this. The wavelength of the X-ray was 1.02 Angstrom and the respective f''and f' values for the metals are +1.66e/+0.30e (Fe), +1.62/-0.5 (Ru) and +2.95/-0.76 (Ga). Is it possible to distinguish between Ru/Ga and Fe and thus to prove that Fe was not bound? The resolution is moderate with 3.1 angstrom and all metals are able to exhibit the same coordination geometry, thus you cannot distinguish according to the geometry. Unfortunately, I was also not able to measure the crystal with multiple wavelenghts because the crystals were very fragile. I hope you can help me and give me some advice. Thank you in advance. Best Regards, Aleks -- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 1090 Wien Tel: +43 1 4277 52536 e-Mail:[email protected]

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mailing list
by Aleksandar Bijelic 01 Jul '14

01 Jul '14

aleksandar.bijeli(a)univie.ac.at -- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 1090 Wien Tel: +43 1 4277 52536 e-Mail:[email protected]

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select sphere syntax
by Tanner, John J. 28 Jun '14

28 Jun '14

Is there a way to select a sphere of residues in the phenix.superpose_pdbs command, analogous to the "around" syntax in cns? I tried "within" and "around" in phenix.superpose_pdbs but got "Atom selection syntax error". Thanks. Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: tannerjj(a)missouri.edu<mailto:[email protected]> phone: 573-884-1280 fax: 573-882-2754 http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

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Coot DNA names
by Bradley Hintze 27 Jun '14

27 Jun '14

Hey Folks, Does anybody know a quick way to convert DNA atom names back to PDB standard after coot modifies them to match the ccp4 dictionary? Thanks -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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quick R-value calculation
by Patrick Loll 27 Jun '14

27 Jun '14

I have a structure pulled from the PDB that contains a gnarly, complex ligand, for which I don't have a library. I just want to do a quick R-value calculation +/- ligand, and I don't want to go to the trouble of building and testing a library just for this purpose. Is there some way to induce phenix.refine or phenix.model_vs_data to do the R-value calculation even if it doesn't recognize the nonbonded energy type symbols? Thanks for any tips. Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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seeking help about running SCALEPACK2mtz
by chen c 26 Jun '14

26 Jun '14

Dear PHENIXBBers: I'e got a problem about data processing when running SCALEPACK2mtz. Hope you can give me some advice on that. Here's my problem: I have an .sca file processed by HKL2000 about 4 years ago, I just ran the Scalepack2mtz program in order to transform it into .mtz file. However, the program keeps running. To ensure that the Scalepack2mtz program is ok, I use another .sca file for verification and it turns out that this file for verification is successfully transformed into .mtz file within seconds. I checked the .log file, the program keeps running when there are the following messeages: "Mean acentric moments I from input data: <I^2>/^2 = 2.360 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 9.187 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 52.348 (Expected value = 24.000, Perfect Twin = 7.500) Mean acentric moments I from anisotropically corrected data: <I^2>/^2 = 3.121 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 12.788 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 57.952 (Expected value = 24.000, Perfect Twin = 7.500) " does this means that the .sca file isn't processed properly? I also checked the scale.log file, and there are the following messages: " Shell Summary of observation redundancies: Lower Upper % of reflections with given No. of observations limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19 >19 total 50.00 5.60 5.9 6.1 18.0 15.1 26.9 19.7 8.3 0.0 0.0 0.0 94.1 5.60 4.45 7.9 9.4 13.0 12.9 23.2 27.5 6.1 0.0 0.0 0.0 92.1 4.45 3.88 19.2 5.6 13.3 13.5 20.4 21.9 6.0 0.0 0.0 0.0 80.8 3.88 3.53 31.9 6.5 11.6 11.3 14.9 17.9 5.8 0.0 0.0 0.0 68.1 3.53 3.28 2.4 4.7 11.3 15.3 23.5 34.1 8.7 0.0 0.0 0.0 97.6 3.28 3.08 0.2 3.6 7.0 15.4 23.7 40.1 9.9 0.0 0.0 0.0 99.8 3.08 2.93 0.4 4.4 8.7 16.8 21.1 41.3 7.2 0.0 0.0 0.0 99.6 2.93 2.80 4.2 8.0 12.7 15.2 20.3 33.7 6.0 0.0 0.0 0.0 95.8 2.80 2.69 15.4 9.1 14.0 13.8 19.2 25.2 3.3 0.0 0.0 0.0 84.6 2.69 2.60 31.6 16.2 11.7 14.2 13.7 10.6 2.0 0.0 0.0 0.0 68.4 All hkl 11.8 7.3 12.2 14.4 20.8 27.1 6.4 0.0 0.0 0.0 88.2 " This clearly indicates an ice ring problem in the data-collection process. However, the ice ring problem shouldn't have caused the error during the .sca to .mtz process. In fact, I have use it for structure-solvement, and currently the two R factor is around 30%. However, the large deviation of <I^3>/^3 or <I^4>/^4 do means something wrong. Would you tell me what exact mistakes did I make? Can I use this .sca file for subsequent structure solving and refinement? Great thanks for your help! best regards chen

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Anisotropic B-factor restraints
by Elke De Zitter 26 Jun '14

26 Jun '14

Dear All I'm refining a protein structure with a resolution of 1.25 A, using Phenix GUI version 1.9. I am refining the B-factors for the protein atoms anisotropic and those for the water molecules isotropic. How can I restrain the anisotropic B-factors so that bonded atoms have similar ellipsoids (like the SIMU and DELU commands in Shelx making the atoms moving similarly in direction and amount)? Thanks Elke Elke De Zitter PhD student, KU Leuven Biochemistry, Molecular and Structural Biology Celestijnenlaan 200f - bus 2404, 3001 Leuven Room 00.84, +32 16 3 26530

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Combining phases?
by Yuri 26 Jun '14

26 Jun '14

Dear All, Im struggling with a structure. I have a good native data set with resolution 2.1A and a data set with ok stats collect at low energy trying to extract some anomalous signal from intrinsic sulphur atoms (6/ASU/400aa). Using a model of one of the domains I got a MolRep solution that has somewhat convincing features in the electron density maps some portions of the structure but not in others. I also ran HySS and obtained some coordinates for the 6 sulphur atoms but the map here is uninterpretable. Xtriage suggests the anomalous is only good until about 8A so I am not that surprised. Is there any way I can try to combine my putative MolRep model and phases with the sulphur anomlaous signal and maybe get better maps to build into? If so, how would I do that using PHENIX? thanks for the help -- Yuri Pompeu, Ph.D.

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GRC/GRS Diffraction Methods
by Anastassis Perrakis 25 Jun '14

25 Jun '14

Dear all, I am sorry to send one more post to the already overloaded bb, but please let me remind you for the last time that the deadline for applications for the GRC and the GRS is approaching, and is only three days from now. http://www.grc.org/programs.aspx?id=11654 We are all looking forward to welcome you at Bates College in a month from now, and we do hope for a few more last minute participations: we need all of you to make it as exciting and fun as possible! Best regards, Tassos

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Multiple Metal Sites in Autosol
by Ryan Henry Gumpper 24 Jun '14

24 Jun '14

??Hello All, ?I have a question regarding the metal assignments when using Autosol to process SAD datasets. I am new to field and I want to make sure that I am doing things correctly. My enzyme should contain 2 metal sites, one with Cu and one with Fe. We collected data at the Fe-edge, the Cu-PreEdge, and the Cu-Edge for a comparison. When I tell Autosol to search for 1 Cu site, using the Cu-Edge data, and another heavy atom Fe, it finds 33 sites all Cu with 2 being Fe. Likewise, using the same dataset, when I include S as an additional anomalous scattering moiety, it will find 1 Cu in the correct position and 32 S atoms--my protein does not contain 32 S atoms. Finally, when I include every possibility that was in my crystallization buffer, this includes a fairly high concentration of MgCl2, and I tell it to search for 1 Cu site with the additional heavy atoms being Fe, S, Mg, and Cl, it seems that it is able to assign the Cu correctly, however it now gives Mg coordinated with Cu instead of H2O molecules, and this is not possible. Should I include Mg and Cl in the search? And S? Also, why would it not be finding the Fe? Furthermore, and most importantly, why is it assigning so many heavy atom sites? I am having similar problems with the other two data sets as well. Thank you very much in advance! Regards, Ryan Gumpper

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Re: [phenixbb] Iron (FE2) metalloprotein
by Nathaniel Echols 24 Jun '14

24 Jun '14

On Tue, Jun 24, 2014 at 1:11 AM, Egor Tchesnokov < etchesnokov(a)chemistry.otago.ac.nz> wrote: > Thank you for the comment. > The model I use for Phaser is coming from Sculptor, so it does not have > heteroatoms. > I introduce heteroatom (Fe) only after Phaser. I use Phaser-EP to find it, > eventhough it is obvious from the density. Then I merge Fe and Phaser.pdb > in Coot after which I feed it to ReadySet. So the pdb that I give to Refine > either have Fe with occupancy of 1, <1 or >1 (I tried both). I use PDB > editor to add charge, but the outcome is still the same. After refinement > Fe occupancy is either 1 or very close. > My apologies, I misinterpreted your message. Is this just a case of "name that blob?" If so, I suggest posting images of the density around the iron to the list (and probably ccp4bb as well) asking for suggestions. It's very likely that someone will have encountered similar density before. -Nat

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Iron (FE2) metalloprotein
by Egor Tchesnokov 24 Jun '14

24 Jun '14

Hello, Active site contains iron (FE2) coordinated by three histidines. After Phaser the active site does not contain un-explained green density. After Refinement blobs of various shapes appear in the vicinity and upto 3-4A of active site iron. Refinement is done using occupancy and anomalous of iron options. Buffers do not contain molecules that could fit in those blobs. Any suggestions? Thank you Egor

3 2

Geometry problems
by Yarrow Madrona 23 Jun '14

23 Jun '14

Hello, I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get: bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01 N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc. Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.

3 4

Sulfate at 3-fold axis
by Zhou, Tongqing (NIH/VRC) [E] 23 Jun '14

23 Jun '14

Dear Colleagues, I am refining a structure and there is a SO4 on the 3-fold axis. What I did was to put atom S and O1 on the 3-fold with occ=0.33, and O2 with occ=1, and no O3 and O4 in the pdb (O3 and O4 will be the symmetry of O2). But when I refine it, Phenix complains close non-bounded distances for both S and O1. Is there a way to refine this sulfate? Thanks! Best regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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after updating my system 1.9 1692
by Afshan Begum 23 Jun '14

23 Jun '14

Dear Developers, I am wondering why my system is getting too much slow after update the phenix new version??? before that its take few mints to finish my job but now its take more than 7 hour just finish one job .could you help me regarding this. Many thanks Best Regards AFSHAN

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Update waters and chain ID
by Scott Lovell 19 Jun '14

19 Jun '14

Hi All, I'm refining a structure (dev-1726) that contains 24 protein subunits which are assigned to chains A-X in the PDB file. Chains Y and Z are assigned to a couple of ligands and the ordered solvent molecules are chain w (lower case). I decided to give the "Update waters" option a try during refinement but it seems that the chain ID of the ordered solvent is changed to chain S by default. Since I already have a protein subunit assigned to chain S, the following error is obtained when I try to open the model in Coot (ERROR 39 READ: Duplicate sequence number and insertion code.). To enable visualization of the model in Coot, I can of course manually change the chain ID for the ordered solvent in the output PDB file using a text editor. However, is there a way to override the ordered solvent default chain ID in Phenix to prevent duplication? Thanks, Scott __________________________________ Scott Lovell Ph.D., Director Protein Structure Laboratory University of Kansas Del Shankel Structural Biology Center

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More problems with HEM.cif?
by Yarrow Madrona 19 Jun '14

19 Jun '14

Hello, The HEM.cif in $Phenix/chem_data/mon_lib has ideal angles of 1.337 for single bonds on the vinyl groups. HEM CAC CBC coval 1.337 0.02 HEM CAB CBB coval 1.337 0.02 As far as I know these are single bonds and the ideal bond angles should be around 1.5. -Yarrow

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Rigid ligand placement into density map
by Phan, Jason 19 Jun '14

19 Jun '14

Hi All, Is there an option or flag in Phenix LigandFit to place the ligand rigidly with pre-generated conformations without torsional adjustments? Would setting "conformers = 1" and "refine_ligand = false" work? Coot Find Ligand with the "flexible" option unchecked seems to work but it won't tell you which original conformer (SD file) the "fitted ligand" comes from since all the conformers have the same residue name and number. Coot doesn't write out SD format either so any ID associated with the original conformer is lost. Jason

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molprobity coot TODO python script
by wtempel 19 Jun '14

19 Jun '14

Hello, I noticed the following when loading a phenix-created python TODO script using the 4730 and 5100 Linux-x86_64-ubuntu-12.04.3-python-gtk2 coot builds. A "MolProbity to-do list" window opens. GUI functions such as "Show Probe dots" and "Overlap only" are working as expected. Clicking anywhere within the "C-beta outliers" or "Severe clashes" areas of the window moves the display center to problem areas of the structure. But: no text is visible in any of the columns ("Chain", "Residue", "Name", etc. of the "C-beta outliers area"; "Atom 1", Atom 2", "Overlap" of the "Severe clashes"). As a result, I cannot select a specific problem spot for centering. Any ideas? Another molprobity related question: us there a phenix script that produces a list of NQH flip candidates? Thank you, Wolfram Tempel Attached image: Clicking in the white areas on the window in the attached screen grab will move the center of the coot display, but labels for the problem areas are not shown in the window's columns.

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GUI program to calculate effective resolution of a data set
by Alexandre OURJOUMTSEV 19 Jun '14

19 Jun '14

Dear All, Recently, there was a ccp4bb conversation concerning the definition of a ‘real’ (effective) resolution of (incomplete) diffraction data sets. I am happy to announce that a corresponding GUI program EFRESOL is available now and you may download it from the Web site: http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/efresol/Efresol.html http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html The method is described in L.Urzhumtseva, B.P.Klaholz, A.Urzhumtsev (2013) Acta Cryst., D69, 1921-1934. We would like to thank Joel Bard, Tom Peat, Rajan Prabu and especially Boaz Shaanan for testing the original version of the program. With best wishes, Sacha Urzhumtsev

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Re: [phenixbb] special positions
by Yarrow Madrona 18 Jun '14

18 Jun '14

Hi Pavel, It turns out I do have some special positions. Waters sit near a 2 fold axis. I have given them 0.5 occupancy. No error comes up but they simply get kicked out of the electron density. Maybe I should turn off rigid body refinement since I don't need it? Below is a link to a screen shot. https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Yarrow, > > oh good! I'm glad you solved the problem -:) > > All the best, > Pavel > > > On 6/18/14, 8:02 AM, Yarrow Madrona wrote: > > Hi Pavel, > > Thanks for your quick response. It turns out that after I reprocessed a > data set in a higher symetry space group I forgot to use a reference mtz so > the orientation was completely off. I just re-ran phaser and everything > worked fine. I didn't run rigid body refinement after phaser. > > The original error message didn't list the atoms and I am not sure how > it could have any atoms on special positions with the solution being > completely wrong. Probably nothing to worry about. > > -Yarrow > > On Tuesday, June 17, 2014, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Yarrow, >> >> ok, I wish that error message (that I put a while ago, in 2009 to be >> precise) lists those atoms... Can you send me the file so I can tell you >> what these atoms are? >> >> In general, if at rigid-body refinement stage you have atoms at special >> positions it is unlikely to be right. >> >> Pavel >> >> On 6/17/14, 12:56 PM, Yarrow Madrona wrote: >> >>> Hi, >>> >>> I am trying to do rigid body refinement, however I get an error in >>> phenix telling me that there are atoms at special positions. >>> >>> I am not sure how to determine which atoms are at special positions so >>> that I can exclude them from rigid body refinement. Can someone help me >>> with this? Thank you. >>> >>> -Yarrow >>> >> >> >

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Calculate F (model) + Calculate Map Correlation
by George Devaniranjan 18 Jun '14

18 Jun '14

Hi, I am trying to use phenix and I was trying to do the following: Take a PDB, generate a MTZ file using Calculate F (model) and lets call it native.mtz then change a few phi and psi values of the pdb (so its slightly different from the native), run Calculate F (model) model.mtz Now I tried to calculate the CC of the two MTZ using Calculate Map Correlation. I get the following: "Missing at least one map file or label" What am I doing wrong? Thank you, George

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Calculation of RSR for a fragment of PDB
by George Devaniranjan 18 Jun '14

18 Jun '14

Hi everyone, I apologize at the beginning itself as I am new to using PHENIX/X-ray crystallography so this question might not make the most sense but I will try and explain it well. I cut out a part of a map for a PDB fragment using phenix map cut out density resulting in a MTZ file. Now I changed the fragment (changed its phi and psi externally) and want to calculate the RSR [real-space R -factor] for the model based on the old density (to check if I have made things worse or not). how can I go about this? I tried using phenix.refine couldn't get it to work. I have attached the MTZ fragment, the original PDB fragment and the modified PDB fragment. native: nativeFragment.pdb model: modelledFragment.pdb MTZ: cut_out_density.MTZ (I can see mine is worse but I want to quantify that "badness") Thank you, George

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Re: [phenixbb] special positions
by Yarrow Madrona 18 Jun '14

18 Jun '14

Hi Pavel, It turns out I do have some special positions. Waters sit near a 2 fold axis. I have given them 0.5 occupancy. No error comes up but they simply get kicked out of the electron density. Maybe I should turn off rigid body refinement since I don't need it? Below is a link to a screen shot. https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png -Yarrow On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Yarrow, > > oh good! I'm glad you solved the problem -:) > > All the best, > Pavel > > > On 6/18/14, 8:02 AM, Yarrow Madrona wrote: > > Hi Pavel, > > Thanks for your quick response. It turns out that after I reprocessed a > data set in a higher symetry space group I forgot to use a reference mtz so > the orientation was completely off. I just re-ran phaser and everything > worked fine. I didn't run rigid body refinement after phaser. > > The original error message didn't list the atoms and I am not sure how > it could have any atoms on special positions with the solution being > completely wrong. Probably nothing to worry about. > > -Yarrow > > On Tuesday, June 17, 2014, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Yarrow, >> >> ok, I wish that error message (that I put a while ago, in 2009 to be >> precise) lists those atoms... Can you send me the file so I can tell you >> what these atoms are? >> >> In general, if at rigid-body refinement stage you have atoms at special >> positions it is unlikely to be right. >> >> Pavel >> >> On 6/17/14, 12:56 PM, Yarrow Madrona wrote: >> >>> Hi, >>> >>> I am trying to do rigid body refinement, however I get an error in >>> phenix telling me that there are atoms at special positions. >>> >>> I am not sure how to determine which atoms are at special positions so >>> that I can exclude them from rigid body refinement. Can someone help me >>> with this? Thank you. >>> >>> -Yarrow >>> >> >> >

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