- phenixbb - phenix-online.org

pdb_redo
by PC 11 Aug '14

11 Aug '14

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

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command line
by PC 08 Aug '14

08 Aug '14

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RNA 5' end needs 2 PO4s
by Phoebe A. Rice 07 Aug '14

07 Aug '14

I'm trying to model the first residue of an RNA, which has a di (maybe tri) phosphate on the 5' end I'm sure someone has already worked this out ... should we call the 1st residue GDP or GTP, and somehow tell phenix about the bond to residue #2 (how?) or should we add pyrophosphate to the default 5' phosphate? PS - as a side point, elbow generates GMP with no phosphate thanks, Phoebe

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CIF for Thiol-substituted DNA
by Mark A. White 06 Aug '14

06 Aug '14

Hello, I have a diThiol substituted phosphate on a CYT residue (C2S: S1P & S2P in place of O1P & O2P). So far I have tried using phenix.elbow to produce a CIF, but with limited success. First, the links to the neighbouring nucleotides are not created. I could just add a links.cif to the input, but this would not include the DNA angle restraints. Second, the sugar-base chirality is not preserved, although it is listed in the CIF file. Is there a better way to produce a substituted DNA, similar to the example of adding the O5T to 5pho GUA? Also, why is the sugar-base chirality not preserved if it is in the CIF? C2S chir_03 C1' O4' N1 C2' positiv the comand: phenix.elbow --do-all dt15_C.pdb produced: elbow.C2S.dt15_C_pdb.001.cif Thanks, Mark -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (281) 734-3614 Fax. (409) 747-1404 mailto://[email protected] http://xray.utmb.edu QQ: "All opinions are not equal. Some are a very great deal more robust, sophisticated and well supported in logic and argument than others." - Douglas Noel Adams (2002)

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elbow, how to get partial charges in mol2 output file?
by Florian Nachon 06 Aug '14

06 Aug '14

Dear phenixbbers, The partial charges are not written in mol2 output files generated by elbow. Is there any way to change that behavior? Probably by editing tripos_mol2_writer.py? Thanks for helping. Florian -- La chance ne sourit qu'aux esprits bien préparés. Louis Pasteur

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Re: [phenixbb] PEG dependent structural changes in crystal structure
by shivendra singh 05 Aug '14

05 Aug '14

Dear Dr. Van Raaji and Dr. Domínguez, Thank you very much for your reply. The salt and pH of crystallisation recipe were same except PEG avg. mol wt. I agree, it may be due to different crystal packing but i am wondering whether disorderedness observed was intrinsic to the protein under PEG1500 or induced by different crystal packing. Also, is it possible that it may be the molten globule state of this protein? I read somewhere that its almost impossible to crystallise molten globule of any protein due to its transient nature. Is it possible that under the PEG1500 environment this collapsed state is more stable? Also looking at its active site, we are sure that it cant be in active form so i am not sure what may be its significance. Also if its a different conformation of active enzyme so is it possible to find out that whether its prior or later state of native form. The function of this enzyme is not related to polyols but hydrolyze cyclic amide substrate. Kind regards Shiv On 6 August 2014 00:23, shivendra singh <shivendra22(a)gmail.com> wrote: > 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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Phenix/DivCon: IUCr & ACS conferences
by Lance Westerhoff 05 Aug '14

05 Aug '14

Hello all- If you are attending the International Union of Crystallography conference in Montreal this week, be sure to stop by our booth and say hello (we are sharing booth #229 with CCG). We will be there to discuss QuantumBio’s quantum mechanics plugin to Phenix, and we will also be presenting results from some of our recent work with Phenix/DivCon. If you would like more information on our activities at the conference, please take a look at the following link: http://www.quantumbioinc.com/news/show/IUCr-2014 And for those of you planning to attend the American Chemical Society meeting in San Francisco next week, we’ll be there as well (yeah, this will be a busy couple of weeks!). I will be presenting a talk on the subject of quantum mechanics based refinement and its impact on drug discovery efforts. More information is available here: http://www.quantumbioinc.com/news/show/ACS-2014-CA Incidentally, we have a new release of our Phenix plugin coming out. If you are not yet a user and you would like to check it out, certainly feel free contact me for more information. Release Notes: http://www.quantumbioinc.com/news/show/Update-6.0.8 We look forward to seeing you! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

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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

1 0

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

2 1

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 22 Jul '14

22 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 22 Jul '14

22 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.

2 1

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

2 2

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

2 1

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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