- phenixbb - phenix-online.org

extend R-free set to higher resolution
by NATHAN THOMSEN 25 Sep '09

25 Sep '09

Is there a phenix utility to extend a phenix generated R-free set to higher resolution (while still using lattice symmetry etc.)? Thanks! Nathan Thomsen UC Berkeley

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Re: [phenixbb] extend R-free set to higher resolution
by Thomas C. Terwilliger 25 Sep '09

25 Sep '09

Hi Nathan, Yes, you can use the GUI to do this (you need a recent nightly build to do it). Just click on "Reflection file editor" and you get an option to extend a free R set, maintaining the free R set you already have. All the best, Tom T >> Is there a phenix utility to extend a phenix generated R-free set to >> higher resolution (while still using lattice symmetry etc.)? Thanks! >> >> Nathan Thomsen >> UC Berkeley >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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wxu_scale is ignored with TLS
by Joe Krahn 25 Sep '09

25 Sep '09

When using TLS, the wxu_scale is changed, even if it is given in the input file. IMHO, TLS should only modify the default value, and not a user-defined wxu_scale. Thanks, Joe Krahn

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Various problems with phenix.refine
by Joe Krahn 25 Sep '09

25 Sep '09

Here are a few problems I have found using phenix.refine 1.4: If NCS restraint selection in the .def file have newline characters, the REMARK 3 formatting is messed up. It should probably replace all white-space regions with a single space. When NCS restraints contain a residue with alternate conformations, that residue gets excluded from all equivalences, even if the selections contain ALTID to avoid the redundant atoms. If the .def file has a syntax error, phenix.refine dies with an error that the file format is not recognized. Why not print syntax errors? The optimize_wxc and optimize_wxu features are useful, but it is difficult to use the result to define an improved fixed scale on subsequent rounds, without having to optimize every time. It is not obvious whether the scale written in the log represents the new wxc_scale, or if it is a multiplier versus the current wxc_scale. The log also truncates to 2 decimal places. In my case, I only get one significant digit from scale=0.05. I propose that the optimizations write something like "Optimal wxc_scale = 0.533". The input data is written as "refine_data.mtz", not using the serial number, and there seems to be no flag to disable writing it. That means I have to force overwrite to run iterations in the same directory. If each run is in its own directory, the serial number is not very useful for filenames. So, the output MTZ should have the serial number, and you might also consider an option to disable the serial number when separate directories are used. Thanks, Joe Krahn

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specifying column labels for input MTZ file
by Tirumala Kumar Chowdary 24 Sep '09

24 Sep '09

Hi, I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). Phenix.refine stopped at 'Multiple equally suitable arrays of observed xray data found. Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav Please use refinement.input.xray_data.labels' Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it. Thanks Tirumal

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question about rfree flag transfer
by crystallogrphy 23 Sep '09

23 Sep '09

Hi, I have built a model against a 3.7A data set by AutoBuild. The resulting model is overall_best.pdb. The data with the rfree test flags is exptl_fobs_phases_freeR_flags.mtz Later on, I got a 3.4A data, which is isomorphous with the 3.7A data. Now I want to transfer the rfree flag from the 3.7A to 3.4A data for refinement. I know one strategy if the data file is in CNS format. That is, use DATAMAN to transfer the flags and generate new test set flags in the high resolution range: 3.7-3.4A. However, when I convert the format by phenix.reflection_file_converter, it fails: phenix.reflection_file_converter exptl_fobs_phases_freeR_flags.mtz --cns=exptl_fobs_phases_freeR_flags.cv --label="PHIM" --label="FP,SIGFP" --label="FOMM" --label="FreeR_flag" --label="FC" However, the resulting data does not have any FP, SIGFP, and FreeR flags. { file: exptl_fobs_phases_freeR_flags.cv.cns } { sg=C2 a=175.385 b=102.472 c=92.057 alpha=90 beta=111.312 gamma=90 } { source of data: exptl_fobs_phases_freeR_flags.mtz:FC } NREFlections=15307 ANOMalous=FALSe DECLare NAME=DATA DOMAin=RECIprocal TYPE=REAL END INDEx 0 0 5 DATA= 0 INDEx 0 0 7 DATA= 0 INDEx 0 0 8 DATA= 0 INDEx 0 0 9 DATA= 0 INDEx 0 0 10 DATA= 0 INDEx 0 0 11 DATA= 0 INDEx 0 0 12 DATA= 0 INDEx 0 0 13 DATA= 0 I also tried mtz2various in CCP4i, the resulting hkl file does not have rfree flags at all. Does anyone know who to convert the exptl_fobs_phases_freeR_flags.mtz into cns format or simple transfer the flags by phenix?

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supported compilers for source builds
by Ben Eisenbraun 22 Sep '09

22 Sep '09

For compiling PHENIX from source, what are the supported compilers? Are the Intel or Portland compilers supported? There are notes in the list archives about using OpenMP with gcc, and hints that the Intel compiler is supported, but I didn't see any docs on building with icc/ifort. In one email Ralf mentions that you might actually lose performance compiling your own version of Solve/Resolve because gfortran optimizes poorly, which leads me to think that the distributed binaries are using ifort for at least the Solve/Resolve bits. Did I overlook some notes on how to do this? -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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question about composite SA_omit map in phenix
by crystallogrphy 22 Sep '09

22 Sep '09

Hi, I am using molecular replacement to build a model against a 2.2A resolution data set. However, the template model only has 23% sequence identity. First, I use chainsaw in CCP4i to prune all side chain to be poly-Ala except the identical residues. Then I use AutoMR and rigid body refinement, I got Rfree=50%. The continuous electron density is not bad showing second structures. However, the model has some out-of-registration problem, for example, two proline are in a alpha-helix. In other words, it has model bias. I want to use composite SA-omit to get a less model bias map, not a simple composite omit map or a SA_omit map ommiting a part of the region. Does someone know who to do this? Thanks! Qun Wan postdoc fellow Case Western Reserve University

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heavy atom in pdb for refinement
by crystallogrphy 20 Sep '09

20 Sep '09

Hi, I have Zn atoms in my pdb for refinement. However, it failed with the following scripts. Do I have to create a libary of this heavy atom? Number of atoms with unknown nonbonded energy type symbols: 6 "ATOM 1 Zn Zn Z 1 .*. Zn " "ATOM 2 Zn Zn Z 2 .*. Zn " "ATOM 3 Zn Zn Z 3 .*. Zn " "ATOM 4 Zn Zn Z 4 .*. Zn " "ATOM 5 Zn Zn Z 5 .*. Zn " "ATOM 6 Zn Zn Z 6 .*. Zn " Time building chain proxies: 1.78, per 1000 atoms: 0.45 Here is the format of my pdb: ..... ATOM 1 Zn Zn Z 1 32.028 47.603 13.955 1.00 30.00 Zn ATOM 2 Zn Zn Z 2 29.017 71.434 8.164 1.00 30.00 Zn ATOM 3 Zn Zn Z 3 39.223 49.330 -6.810 1.00 30.00 Zn ATOM 4 Zn Zn Z 4 24.811 89.144 -4.406 1.00 30.00 Zn ATOM 5 Zn Zn Z 5 23.652 72.429 6.125 1.00 30.00 Zn ATOM 6 Zn Zn Z 6 30.132 63.054 -31.918 1.00 30.00 Zn TER 7 Zn 6 ATOM 10 CL CL L 1 20.125 63.405 10.719 1.00 30.00 CL TER 11 CL 1

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RuntimeError : min()
by RAVINDRA D MAKDE 19 Sep '09

19 Sep '09

Hi all, I will highly appreciate your help to resolve the following bugs encountered during running phenix.refine on GUI as well as on command lines. My version of Phenix and platform are: PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 3 cctbx tag: 2008_12_07_1353 Platform: mac-intel-osx osx-10.5.8 The error encountered using phenix refinement GUI (phenix.refine_gui) is as follows: A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks!RuntimeError : min() argument is an empty arrayTraceback:Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Base.py", line 274, in OnBrowse self.file_text_field.SetValue(new_path) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Controls.py", line 974, in SetValue self.phil_handler.propagate_update(self.phil_def_name, new_value) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/PhilInterfaceHandler.py", line 103, in propagate_update self._update_handlers[def_name](self, def_name, value) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Extensions.py", line 28, in extract_xray_neutron_params phil_def_name = phil_object_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 155, in __init__ self.load_reflection_file(file_name, phil_def_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 159, in load_reflection_file self.hkl_server = self.hkl_handler.add_hkl_file(file_name, phil_def_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 66, in add_hkl_file err=sys.stderr) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0): The error encountered using phenix refinement on command line (phenix.refine coordinate.pdb reflection.mtz) is as follows: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0):RuntimeError: min() argument is an empty array N.B. Earlier, I had encountered the similar error (using command line) using PHENIX version 1.3 on the same platform. Thanks in advance. Regards, Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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Re: [phenixbb] xtriage to double-check symmetry
by Frank von Delft 18 Sep '09

18 Sep '09

>>>> >>>> So I thought I'd listen to xtriage: seemed easy since I have both >>>> data >>>> and model in P6522, and I ran: >>>> phenix.xtriage final.mtz reference.structure.file=final.pdb >>>> > Uh-oh.... what I meant is, I have both data and model in ==>P65<==. (Bad typo -- explains Peter's patient but puzzled response, which did however confirm I'd understood correctly after all :) So, again: I have *some* lower symmetry (not P1, though); should I expect xtriage to print out tests for P6522 somewhere? Because I don't find it. <later> That said: after updating phenix to 1.4-162, I now do find that table in the output (attached, last table), and it seems we're in-between: seems we have probably indeed missed the two-fold, so now we must figure out why it "didn't refine" in P6522. Thanks for you help and explanation! phx. > But isn't P6522 already the highest symmetry? I think if you run X-triage > on the data reduced as P65, it will as you say check the extra operations > implied by p6522 and see if they are justified. > If the data is already reduced in p6522, those reflections have already > been merged and there is no way to tell how good the agreement was? > > I don't think xtriage will look at your model- but then I've never > given it a model. > I would guess from your lower Rfree in P65 that it is the lower symmetry- > the 2-fold operators that make it almost fit p6522 are psuedosymmetry, > noncrystallographic symmetry that almost fits the p6522 operators but > not quite. > > Best, > Ed ############################################################# ## phenix.xtriage ## ## ## ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## ## ## ############################################################# #phil __OFF__ Date 2009-09-18 Time 08:19:32 BST +0100 (1253258372.97 s) ##-------------------------------------------## ## WARNING: ## ## Number of residues unspecified ## ##-------------------------------------------## Effective parameters: #phil __ON__ scaling { input { asu_contents { n_residues = None n_bases = None n_copies_per_asu = None } xray_data { file_name = "final.mtz" obs_labels = None calc_labels = None unit_cell = 81.38990021 81.38990021 79.47530365 90 90 120 space_group = "P 65" high_resolution = None low_resolution = None reference { data { file_name = None labels = None unit_cell = None space_group = None } structure { file_name = "final.pdb" } } } parameters { reporting { verbose = 1 log = "logfile.log" ccp4_style_graphs = True } misc_twin_parameters { missing_symmetry { sigma_inflation = 1.25 } twinning_with_ncs { perform_analyses = False n_bins = 7 } twin_test_cuts { low_resolution = 10 high_resolution = None isigi_cut = 3 completeness_cut = 0.85 } } } optional { hklout = None hklout_type = mtz sca *mtz_or_sca label_extension = "massaged" aniso { action = *remove_aniso None final_b = *eigen_min eigen_mean user_b_iso b_iso = None } outlier { action = *extreme basic beamstop None parameters { basic_wilson { level = 1e-06 } extreme_wilson { level = 0.01 } beamstop { level = 0.001 d_min = 10 } } } symmetry { action = detwin twin *None twinning_parameters { twin_law = None fraction = None } } } } gui { result_file = None } } #phil __END__ Symmetry, cell and reflection file content summary Miller array info: final.mtz:F,SIGF Observation type: xray.amplitude Type of data: double, size=15235 Type of sigmas: double, size=15235 Number of Miller indices: 15235 Anomalous flag: False Unit cell: (81.3899, 81.3899, 79.4753, 90, 90, 120) Space group: P 65 (No. 170) Systematic absences: 0 Centric reflections: 606 Resolution range: 35.2429 2.20034 Completeness in resolution range: 0.999344 Completeness with d_max=infinity: 0.999082 ##----------------------------------------------------## ## Basic statistics ## ##----------------------------------------------------## Matthews coefficient and Solvent content statistics Number of residues unknown, assuming 50% solvent content ---------------------------------------------------------------- | Best guess : 278 residues in the asu | ---------------------------------------------------------------- Completeness and data strength analyses The following table lists the completeness in various resolution ranges, after applying a I/sigI cut. Miller indices for which individual I/sigI values are larger than the value specified in the top row of the table, are retained, while other intensities are discarded. The resulting completeness profiles are an indication of the strength of the data. ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 35.25 - 5.42 | 99.9% | 98.8% | 97.7% | 96.5% | 94.7% | 92.0% | | 5.42 - 4.30 | 100.0% | 99.1% | 97.9% | 97.1% | 94.6% | 91.8% | | 4.30 - 3.76 | 100.0% | 99.3% | 98.0% | 96.6% | 93.4% | 89.4% | | 3.76 - 3.42 | 100.0% | 98.9% | 96.2% | 93.5% | 87.1% | 80.7% | | 3.42 - 3.17 | 100.0% | 95.2% | 91.3% | 87.4% | 76.8% | 62.0% | | 3.17 - 2.99 | 100.0% | 93.7% | 86.3% | 76.9% | 60.7% | 45.2% | | 2.99 - 2.84 | 100.0% | 88.3% | 73.8% | 60.3% | 37.7% | 19.2% | | 2.84 - 2.71 | 100.0% | 83.5% | 66.6% | 50.2% | 24.2% | 11.4% | | 2.71 - 2.61 | 100.0% | 75.9% | 55.7% | 41.2% | 18.0% | 6.9% | | 2.61 - 2.52 | 99.9% | 69.8% | 44.4% | 28.7% | 10.9% | 5.2% | | 2.52 - 2.44 | 99.5% | 61.0% | 34.9% | 19.6% | 8.2% | 3.9% | | 2.44 - 2.37 | 98.6% | 57.6% | 28.8% | 15.8% | 5.8% | 2.6% | | 2.37 - 2.31 | 98.8% | 44.3% | 20.0% | 11.2% | 4.7% | 2.0% | | 2.31 - 2.25 | 99.2% | 31.5% | 14.4% | 7.6% | 3.4% | 0.8% | ---------------------------------------------------------------------------------------- The completeness of data for which I/sig(I)>3.00, exceeds 85% for resolution ranges lower than 2.99A. The data are cut at this resolution for the potential twin tests and intensity statistics. Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of None: 49.24 A**(-2) Estimated -log of scale factor of None: 0.40 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of None: 51.68, -0.00, 0.00 51.68, -0.00 44.95 Equivalent representation as U_cif: 0.65, 0.33, -0.00 0.65, 0.00 0.57 Eigen analyses of B-cart: Value Vector Eigenvector 1 : 51.675 ( 0.91, -0.42, 0.00) Eigenvector 2 : 51.675 ( 0.42, 0.91, -0.00) Eigenvector 3 : 44.948 (-0.00, 0.00, 1.00) ML estimate of -log of scale factor of None: 0.40 Correcting for anisotropy in the data Some basic intensity statistics follow. Low resolution completeness analyses The following table shows the completeness of the data to 5 Angstrom. unused: - 35.2437 [ 0/4 ] 0.000 bin 1: 35.2437 - 10.6916 [138/139] 0.993 bin 2: 10.6916 - 8.5258 [136/136] 1.000 bin 3: 8.5258 - 7.4597 [127/127] 1.000 bin 4: 7.4597 - 6.7830 [133/133] 1.000 bin 5: 6.7830 - 6.2998 [133/133] 1.000 bin 6: 6.2998 - 5.9302 [133/133] 1.000 bin 7: 5.9302 - 5.6345 [131/131] 1.000 bin 8: 5.6345 - 5.3901 [128/128] 1.000 bin 9: 5.3901 - 5.1832 [133/133] 1.000 bin 10: 5.1832 - 5.0049 [137/137] 1.000 unused: 5.0049 - [ 0/0 ] Mean intensity analyses Analyses of the mean intensity. Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. The following resolution shells are worrisome: ------------------------------------------------ | d_spacing | z_score | compl. | <Iobs>/<Iexp> | ------------------------------------------------ | 6.201 | 5.09 | 1.00 | 0.681 | ------------------------------------------------ Possible reasons for the presence of the reported unexpected low or elevated mean intensity in a given resolution bin are : - missing overloaded or weak reflections - suboptimal data processing - satellite (ice) crystals - NCS - translational pseudo symmetry (detected elsewhere) - outliers (detected elsewhere) - ice rings (detected elsewhere) - other problems Note that the presence of abnormalities in a certain region of reciprocal space might confuse the data validation algorithm throughout a large region of reciprocal space, even though the data are acceptable in those areas. Possible outliers Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 Acentric reflections: ----------------------------------------------------------------- | d_space | H K L | |E| | p(wilson) | p(extreme) | ----------------------------------------------------------------- | 3.054 | 0, 1, 26 | 5.09 | 5.35e-12 | 7.77e-08 | ----------------------------------------------------------------- p(wilson) : 1-(1-exp[-|E|^2]) p(extreme) : 1-(1-exp[-|E|^2])^(n_acentrics) p(wilson) is the probability that an E-value of the specified value would be observed if it were selected at random the given data set. p(extreme) is the probability that the largest |E| value is larger or equal than the observed largest |E| value. Both measures can be used for outlier detection. p(extreme) takes into account the size of the dataset. Centric reflections: ----------------------------------------------------------------- | d_space | H K L | |E| | p(wilson) | p(extreme) | ----------------------------------------------------------------- | 6.408 | 0, 11, 0 | 3.81 | 1.38e-04 | 7.72e-02 | ----------------------------------------------------------------- p(wilson) : 1-(erf[|E|/sqrt(2)]) p(extreme) : 1-(erf[|E|/sqrt(2)])^(n_acentrics) p(wilson) is the probability that an E-value of the specified value would be observed when it would selected at random from the given data set. p(extreme) is the probability that the largest |E| value is larger or equal than the observed largest |E| value. Both measures can be used for outlier detection. p(extreme) takes into account the size of the dataset. Ice ring related problems The following statistics were obtained from ice-ring insensitive resolution ranges mean bin z_score : 1.55 ( rms deviation : 1.28 ) mean bin completeness : 1.00 ( rms deviation : 0.00 ) The following table shows the z-scores and completeness in ice-ring sensitive areas. Large z-scores and high completeness in these resolution ranges might be a reason to re-assess your data processsing if ice rings were present. ------------------------------------------------ | d_spacing | z_score | compl. | Rel. Ice int. | ------------------------------------------------ | 3.897 | 0.17 | 1.00 | 1.000 | | 3.669 | 2.93 | 1.00 | 0.750 | | 3.441 | 2.03 | 1.00 | 0.530 | | 2.671 | 3.02 | 1.00 | 0.170 | | 2.249 | 2.71 | 1.00 | 0.390 | ------------------------------------------------ Abnormalities in mean intensity or completeness at resolution ranges with a relative ice ring intensity lower than 0.10 will be ignored. No ice ring related problems detected. If ice rings were present, the data does not look worse at ice ring related d_spacings as compared to the rest of the data set. Basic analyses completed ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 2.99 Angstrom. Determining possible twin laws. The following twin laws have been found: -------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | -------------------------------------------------------------------------------- | M | 2-fold | 0.000 | 0.000 | 0.000 | h,-h-k,-l | -------------------------------------------------------------------------------- M: Merohedral twin law PM: Pseudomerohedral twin law 1 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 1 twin operator were found Details of automated twin law derivation ---------------------------------------- Below, the results of the coset decomposition are given. Each coset represents a single twin law, and all symmetry equivalent twin laws are given. For each coset, the operator in (x,y,z) and (h,k,l) notation are given. The direction of the axis (in fractional coordinates), the type and possible offsets are given as well. Furthermore, the result of combining a certain coset with the input space group is listed. This table can be usefull when comparing twin laws generated by xtriage with those listed in lookup tables In the table subgroup H denotes the *presumed intensity symmetry*. Group G is the symmetry of the lattice. Left cosets of : subgroup H: P 6 and group G: P 6 2 2 Coset number : 0 (all operators from H) x,y,z h,k,l Rotation: 1 ; direction: (0, 0, 0) ; screw/glide: (0,0,0) -x,-y,z -h,-k,l Rotation: 2 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) -y,x-y,z k,-h-k,l Rotation: 3 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) -x+y,-x,z -h-k,h,l Rotation: 3 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) x-y,x,z h+k,-h,l Rotation: 6 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) y,-x+y,z -k,h+k,l Rotation: 6 ; direction: (0, 0, 1) ; screw/glide: (0,0,0) Coset number : 1 (H+coset[1] = P 6 2 2) x-y,-y,-z h,-h-k,-l Rotation: 2 ; direction: (1, 0, 0) ; screw/glide: (0,0,0) -y,-x,-z -k,-h,-l Rotation: 2 ; direction: (-1, 1, 0) ; screw/glide: (0,0,0) x,x-y,-z h+k,-k,-l Rotation: 2 ; direction: (2, 1, 0) ; screw/glide: (0,0,0) -x,-x+y,-z -h-k,k,-l Rotation: 2 ; direction: (0, 1, 0) ; screw/glide: (0,0,0) y,x,-z k,h,-l Rotation: 2 ; direction: (1, 1, 0) ; screw/glide: (0,0,0) -x+y,y,-z -h,h+k,-l Rotation: 2 ; direction: (1, 2, 0) ; screw/glide: (0,0,0) Note that if group H is centered (C,P,I,F), elements corresponding to centering operators are omitted. (This is because internally the calculations are done with the symmetry of the reduced cell) Splitting data in centrics and acentrics Number of centrics : 306 Number of acentrics : 5664 Patterson analyses ------------------ Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.000 0.000 0.239 Distance to origin : 18.971 Height (origin=100) : 7.557 p_value(height) : 4.031e-01 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 4.031e-01. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Systematic absences ------------------- The following table gives information about systematic absences. For each operator, the reflections are split in three classes: Absent : Reflections that are absent for this operator. Non Absent: Reflection of the same type (i.e. (0,0,l)) as above, but they should be present. Complement: All other reflections. For each class, the <I/sigI> is reported, as well as the number of 'violations'. A 'violation' is designated as a reflection for which a I/sigI criterion is not met. The criteria are Absent violation : I/sigI > 3.0 Non Absent violation : I/sigI < 3.0 Complement violation : I/sigI < 3.0 Operators with low associated violations for *both* absent and non absent reflections, are likely to be true screw axis or glide planes. Both the number of violations and their percentages are given. The number of violations within the 'complement' class, can be used as a comparison for the number of violations in the non-absent class. ------------------------------------------------------------------------------------------------------------------------------------------- | Operator | absent under operator | | not absent under operator | | all other reflections | | | | | <I/sigI> (violations) | n absent | <I/sigI> (violations) | n not absent | <I/sigI> (violations) | n compl | Score | ------------------------------------------------------------------------------------------------------------------------------------------- | 6_0 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_1 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_2 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_3 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_4 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | | 6_5 (c) | 0.00 (0, 0.0%) | 0 | 22.42 (0, 0.0%) | 3 | 28.44 (303, 5.1%) | 5967 | 1.14e+00 | ------------------------------------------------------------------------------------------------------------------------------------------- Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of absent violations are listed under the '+++' column. The number of present violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ----------------------------------------------------------------------------------- | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 6 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 61 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 65 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 62 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 64 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 63 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | ----------------------------------------------------------------------------------- Wilson ratio and moments Acentric reflections <I^2>/<I>^2 :2.073 (untwinned: 2.000; perfect twin 1.500) <F>^2/<F^2> :0.776 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.750 (untwinned: 0.736; perfect twin 0.541) Centric reflections <I^2>/<I>^2 :3.729 (untwinned: 3.000; perfect twin 2.000) <F>^2/<F^2> :0.580 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :1.089 (untwinned: 0.968; perfect twin 0.736) NZ test (0<=z<1) to detect twinning and possible translational NCS ----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.104 | 0.095 | 0.320 | 0.248 | | 0.2 | 0.194 | 0.181 | 0.438 | 0.345 | | 0.3 | 0.267 | 0.259 | 0.474 | 0.419 | | 0.4 | 0.342 | 0.330 | 0.487 | 0.474 | | 0.5 | 0.402 | 0.394 | 0.542 | 0.520 | | 0.6 | 0.463 | 0.451 | 0.621 | 0.561 | | 0.7 | 0.512 | 0.503 | 0.641 | 0.597 | | 0.8 | 0.564 | 0.551 | 0.683 | 0.629 | | 0.9 | 0.603 | 0.593 | 0.703 | 0.657 | | 1.0 | 0.644 | 0.632 | 0.712 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.014 | | Maximum deviation centric : 0.093 | | | | <NZ(obs)-NZ(twinned)>_acentric : +0.010 | | <NZ(obs)-NZ(twinned)>_centric : +0.044 | ----------------------------------------------- L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.501 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.336 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. --------------------------------------------- Analysing possible twin law : h,-h-k,-l --------------------------------------------- Results of the H-test on acentric data: (Only 50.0% of the strongest twin pairs were used) mean |H| : 0.012 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.000 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.488 Estimation of twin fraction via cum. dist. of H: 0.489 Britton analyses Extrapolation performed on 0.47 < alpha < 0.495 Estimated twin fraction: 0.453 Correlation: 0.9692 R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.015 R_abs_twin calculated data : 0.018 R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.000 R_sq_twin calculated data : 0.000 Perfoming correlation analyses The supplied calculated data are normalized and artificially twinned Subsequently a correlation with the observed data is computed. Results: Correlation : 0.828109216467 Estimated twin fraction : 0.47 Maximum Likelihood twin fraction determination Zwart, Read, Grosse-Kunstleve & Adams, to be published. The estimated twin fraction is equal to 0.478 Exploring higher metric symmetry The point group of data as dictated by the space group is P 6 the point group in the niggli setting is P 6 (c,a,b) The point group of the lattice is P 6 2 2 (c,a,b) A summary of R values for various possible point groups follow. -------------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | -------------------------------------------------------------------------------------------------- | P 6 2 2 (c,a,b) | 0.015 | 0.015 | None | None | 1.508e+04 | <--- | | P 6 (c,a,b) | None | None | 0.015 | 0.015 | 2.595e+04 | | -------------------------------------------------------------------------------------------------- R_used: mean and maximum R value for symmetry operators *used* in this point group R_unused: mean and minimum R value for symmetry operators *not used* in this point group An automated point group suggestion is made on the basis of the BIC (Bayesian information criterion). The likely point group of the data is: P 6 2 2 (c,a,b) Possible space groups in this point groups are: Unit cell: (81.3899, 81.3899, 79.4753, 90, 90, 120) Space group: P 61 2 2 (No. 178) Unit cell: (81.3899, 81.3899, 79.4753, 90, 90, 120) Space group: P 65 2 2 (No. 179) Note that this analysis does not take into account the effects of twinning. If the data are (almost) perfectly twinned, the symmetry will appear to be higher than it actually is. --------------------------------------------------- Merging in *suggested* point group P 6 2 2 (c,a,b) --------------------------------------------------- R-linear = sum(abs(data - mean(data))) / sum(abs(data)) R-square = sum((data - mean(data))**2) / sum(data**2) In these sums single measurements are excluded. Redundancy Mean Mean Min Max Mean R-linear R-square unused: - 9.9896 bin 1: 9.9896 - 5.9876 1 2 1.665 0.0173 0.0023 bin 2: 5.9876 - 4.9363 1 2 1.733 0.0173 0.0009 bin 3: 4.9363 - 4.3717 1 2 1.767 0.0161 0.0013 bin 4: 4.3717 - 4.0001 1 2 1.789 0.0181 0.0013 bin 5: 4.0001 - 3.7294 1 2 1.817 0.0261 0.0041 bin 6: 3.7294 - 3.5197 1 2 1.805 0.0289 0.0027 bin 7: 3.5197 - 3.3504 1 2 1.827 0.0317 0.0033 bin 8: 3.3504 - 3.2096 1 2 1.831 0.0562 0.0108 bin 9: 3.2096 - 3.0898 1 2 1.831 0.0627 0.0119 bin 10: 3.0898 - 2.9861 1 2 1.847 0.0621 0.0095 unused: 2.9861 - Suggesting various space group choices on the basis of systematic absence analyses Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of absent violations are listed under the '+++' column. The number of present violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ----------------------------------------------------------------------------------- | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 6 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 61 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 65 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 62 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 64 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | P 63 2 2 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | ----------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws <I^2>/<I>^2 : 2.073 <F>^2/<F^2> : 0.776 <|E^2-1|> : 0.750 <|L|>, <L^2>: 0.501, 0.336 Multivariate Z score L-test: 1.562 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. Statistics depending on twin laws ------------------------------------------------------------------------------------ | Operator | type | R_abs obs. | R_abs calc. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------------------------ | h,-h-k,-l | M | 0.015 | 0.018 | 0.453 | 0.489 | 0.478 | ------------------------------------------------------------------------------------ Patterson analyses - Largest peak height : 7.557 (corresponding p value : 0.40308) The largest off-origin peak in the Patterson function is 7.56% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. The symmetry of the lattice and intensity however suggests that the input space group is too low. See the relevant sections of the log file for more details on your choice of space groups. As the symmetry is suspected to be incorrect, it is advicable to reconsider data processing. -------------------------------------------------------------------------------

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xtriage to double-check symmetry
by Frank von Delft 17 Sep '09

17 Sep '09

Hi We were trying to decide whether a structure is P65 or P6522: data merges fine in latter, and NCS is perfect, but R/Rfree are significantly worse (32/37-ish vs 23/28 for P65). So I thought I'd listen to xtriage: seemed easy since I have both data and model in P6522, and I ran: phenix.xtriage final.mtz reference.structure.file=final.pdb I'm not sure it's done anything, though - at least, I can't find the table shown on the 4th-last slide of this presentation: http://aca.hwi.buffalo.edu/HotNews/twinning/zwart.pdf Something I said / did not say? Do I *have* to run it in P1? Thanks! phx

2 3

Autobuild at 5A resolution
by Peter Grey 17 Sep '09

17 Sep '09

Dear Phenix users, I am trying to solve a big RNA/protein complex at 5A resolution. Phases come from MR solution with a partial model in Phaser. Thanks to NCS the map after density modification in RESOLVE is of reasonable quality for this resolution and new secondary structures, out side of the model, can be detected. I would like to improve the maps and model with something like a poor man's version of AutoBuild. An Autobuild for very low resolutions that does not include refinement but iteratively carries out density modification and identification of helices/strands outside of the model with phenix.find_helices_strand. Does this sound feasible, Are there already scripts the follow such a scheme ? Many thanks in advance for your advice -- Peter

3 3

error: running phenix.refine
by RAVINDRA D MAKDE 16 Sep '09

16 Sep '09

Hello all, I will greatly appreciate the help for the following: I am getting the error "RuntimeError: min() argument is an empty array" (more details error message given below) while running phenix.refine. I am using PHENIX: Version: 1.3 on Platform: mac-intel-osx osx-10.5.7 My error message is as follows: Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_utils.py", line 379, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.3-final/iotbx/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.3-final/iotbx/iotbx/mtz/__init__.py", line 424, in as_miller_arrays and flex.min(column_group.sigmas()) > 0):RuntimeError: min() argument is an empty array Thanks in advance, Regards, Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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Problem with modified cysteine CME
by Kendall Nettles 16 Sep '09

16 Sep '09

I am trying to refine a structure with modified cysteines, which refmac recognized as CME just fine. Phenix has CME listed in the mon_lib_list.cif, but the CME.cif file was not in the mon_lib/c/ directory. I added it to the phenix mon_lib/c directory but phenix.refine still complained. I next added the CME.cif file ( copied from ccp4) as a command line input to phenix.refine, and added this to my parameters file: refinement.pdb_interpretation.apply_cif_modification { data_mod = CME residue_selection = chain A and resid 381 residue_selection = chain B and resid 381 residue selection = chain B and resid 530 } Still no luck. Thanks for your help, Kendall -- Kendall W. Nettles, PhD Associate Professor Department of Cancer Biology The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458

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Adding multiple conformers beyond 4
by Ben Mueller 15 Sep '09

15 Sep '09

I am a relatively new Phenix user and I am trying to see if it is possible to push the number of conformers beyond 4. I tried to do so, and I recieved the error message: RuntimeError: Exceed maximum allowable number of conformers (=4). Is there an easy (or difficult) way around this? Thanks for your time, Ben Mueller Phillips Lab Department of Biochemistry University of Wisconsin - Madison

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problems with kicked maps in phenix version 1.4-162
by Sabine Schneider 15 Sep '09

15 Sep '09

Hello, Im trying to generate kicked maps in phenix1.4-162 using the following comand: phenix.refine junk.mtz xray_data.labels=F_XDSdataset,SIGF_XDSdataset \ coot-1.pdb strategy=individual_sites simulated_annealing=true refine2.params where refine2.params is: electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT_kick mtz_label_phases = PH2FOFCWT_kick likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = true } map { mtz_label_amplitudes = FOFCWT_kick mtz_label_phases = PHFOFCWT_kick likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = true } } I get the following error message: refinement.input.xray_data.labels = F_XDSdataset,SIGF_XDSdataset refinement.refine.strategy = individual_sites refinement.main.simulated_annealing = true ******************************************************************************* ERROR: Unused parameter definitions: electron_density_maps.map.mtz_label_amplitudes (file "refine2.params", line 3) electron_density_maps.map.mtz_label_phases (file "refine2.params", line 4) electron_density_maps.map.likelihood_weighted (file "refine2.params", line 5) electron_density_maps.map.obs_factor (file "refine2.params", line 6) electron_density_maps.map.calc_factor (file "refine2.params", line 7) electron_density_maps.map.kicked (file "refine2.params", line 8) electron_density_maps.map.fill_missing_f_obs_with_weighted_f_model (file "refine2.params", line 9) electron_density_maps.map.mtz_label_amplitudes (file "refine2.params", line 12) electron_density_maps.map.mtz_label_phases (file "refine2.params", line 13) electron_density_maps.map.likelihood_weighted (file "refine2.params", line 14) electron_density_maps.map.obs_factor (file "refine2.params", line 15) electron_density_maps.map.calc_factor (file "refine2.params", line 16) electron_density_maps.map.kicked (file "refine2.params", line 17) electron_density_maps.map.fill_missing_f_obs_with_weighted_f_model (file "refine2.params", line 18) ******************************************************************************* Sorry: Unused parameter definitions: Please check the input file(s) for spelling errors and obsolete parameter definitions. To disable this error message, add --unused_ok to the command line arguments. I also tested the input file using : libtbx.phil refine2.params and it seems OK? Would be great if you could tell me where I am going wrong! Thanks a lot for your help in advance! Sabine -- ------------------------------------------ Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Biochemistry Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77752 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/

2 1

A request
by Jonathan Grimes 15 Sep '09

15 Sep '09

Are there plans to implement STRICT NCS refinement in Phenix ?? For virus structures I am stuck with using CNS. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

2 2

omit map with phases
by Jianghai Zhu 14 Sep '09

14 Sep '09

Hi, When I am using phenix.autobuild to calculate an SA_omit map, I found out the phenix.autobuild automatically used the phases in my mtz file. How does phenix.autobuild use the phases? and is it a good idea to use phases in omit map calculation? and what kind of phases are preferred, experimental phases, phases after density modification, and phases after multi-crystal averaging? Thanks. -- Jianghai

2 1

Using SAXS data for phasing at mediocre resolution.
by Francis E Reyes 14 Sep '09

14 Sep '09

Hi all I'm looking for anyone who has had (practical) experience using SAXS data to phase 4.2 A crystals. Please email me. FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

1 0

Sequence file for DNA
by jens j birktoft 12 Sep '09

12 Sep '09

Hi: What is the proper format for a sequence file for double stranded DNA duplex/helix ? Do both strands have to be entered, separated by >'s or just one of the complimentary strands Cheers Jay

2 1

Phaser-Gui question
by Jonathan Grimes 11 Sep '09

11 Sep '09

Dear Developers, As a late developer I have recently started to use the new GUI. Its very impressive but what I would like to do is to fire off a number of jobs to vary parameters say in refinement or auto-rebuilding. I havent been able to work out how to submit multiple jobs via the same configuration tab window. Is this possible ? Am I missing a trick. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

2 3

SA omit map
by Pascal Egea 11 Sep '09

11 Sep '09

Dear All,I have a theoretical/practical question about omit maps and refinement. I am completing the refinement (in Phenix) of a protein-ligand complex at 1.3A resolution. I solved it by MR and automatic rebuilding of the protein alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after TLS and water-picking in Phenix. The model includes everything protein, water, ligand and some ions. However I have some slight doubts one region in my ligand. What would be the best map, less biased, to look at this "very late" stage of the refinement. Are composite or systematic SA omit map useful options at this stage ? Thanks a lot in advance Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-825-1013 lab (310)-825-8722 email pegea(a)mednet.ucla.edu

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Re: [phenixbb] SA omit map
by Thomas C. Terwilliger 11 Sep '09

11 Sep '09

Hi Pascal, I think that if you are only concerned about one ligand then there are four overall options. The first, going back before you added the ligand, is likely to be the least biased, then the iterative-build omit, then the SA-omit and kicked maps. The iterative-build omit map is probably the best way to get rid of bias once it has been introduced, but it is also very computationally intensive. As you are only interested in the ligand, you probably do not need to do a composite map, saving you a lot of time. So the options are: 1. You can go back to the structure you had just prior to adding that ligand, and simply refine that structure and look carefully at the maps. As the structure has never seen the ligand, you have no worries about bias at all in that map. Of course that map may be from a much earlier stage, so it may not be so clear either...leading to the other options of.. 2. Take your current structure and run an SA-omit map or an iterative-build omit map, omitting around a PDB file that you create that contains only the ligand. 3. Or, pretty much equivalent to #2, you can remove your ligand from the structure and just do a run of SA or rebuild-in-place and calculate a map, 4. Or you can calculate a kicked map. For the kicked map, quoting Pavel Afonine: in your parameter file just add another map scope to the electron_density_maps scope, like this: electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_kick" mtz_label_phases = "PHFOFCWT_kick" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } } This will create two additional kick maps in addition to the default maps. All the best, Tom T , >> Dear All,I have a theoretical/practical question about omit maps and >> refinement. >> I am completing the refinement (in Phenix) of a protein-ligand complex at >> 1.3A resolution. I solved it by MR and automatic rebuilding of the protein >> alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after >> TLS and water-picking in Phenix. The model includes everything protein, >> water, ligand and some ions. >> However I have some slight doubts one region in my ligand. >> What would be the best map, less biased, to look at this "very late" stage >> of the refinement. Are composite or systematic SA omit map useful options >> at this stage ? >> >> Thanks a lot in advance >> >> >> Pascal F. Egea, PhD >> Assistant Professor >> UCLA, David Geffen School of Medicine >> Department of Biological Chemistry >> 314 Biomedical Sciences Research Building >> office (310)-825-1013 >> lab (310)-825-8722 >> email pegea(a)mednet.ucla.edu >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

4 4

Auto builiding
by Jonathan Grimes 11 Sep '09

11 Sep '09

Dear Developers, I have a molecular replacement solution with a model that has 58 seq identity to my protein. There is 1 insertion in my protein of 1 residue and 1 deletion of 4 residues compared to the model. There are 2 mols in the asym unit. When I run autobuild with standard settings (but either Auto or Yes for the rebuild in place) it falls over with this error. **************************************** AutoBuild Input failed Sorry, the PDB file and sequence file could not be aligned (with no gaps and >50.0% identity) Please restart the wizard... You have several possibilities to try .... You can set rebuild_in_place=No You can set input_sequence_file=None You can edit your model to make sure it has no residues extending N-terminal of the beginning of the corresponding sequences in your sequence file You can set min_seq_identity_percent to a lower value You can set highest_resno to a higher value You can specify start_chains_list if your PDB file sequence starts with a residue number greater than the number of residues in the sequence. **************************************** It runs with rebuild_in_place=No but given the low resolution of the data (3.5A) I thought it would be best to keep as much of the model as possible. What am I doing wrong. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

2 1

Re: [phenixbb] SA omit map
by Gino Cingolani 11 Sep '09

11 Sep '09

Dear Pascal, my suggestion to convince yourself that your ligand is there ..... 1. omit the atoms corresponding to your ligand from your pdb 2. compute electron density difference maps using data between 15-2.5A. High res maps (1.3-2.5A) will look worst than medium res maps if your ligand is partially occupied/mobile (typically bound on the surface of your proteins as opposed to a cavity). 3. Also, make sure you aren't wiping off the ligand by using an improper solvent masks during solvent flattening. If your ligand is really there, but not quite there.... you may try to pressure freeze your crystals instead of using conventional cryo-protectants. Good luck. Gino

1 0

how to generate anomalous difference map in phenix
by crystallogrphy 10 Sep '09

10 Sep '09

Hi, Does anyone know how to generate anomalous difference map by phenix? I have the data file with the scalepack format and the refined model against this data. Thanks!

3 2

Changing the resolution cutoff for water picking
by Sam Stampfer 10 Sep '09

10 Sep '09

Hi, I'm refining a 2.88 resolution structure and would like to pick waters. I assume the default low_resolution is set to 2.8 Angstroms and so my lower resolution map is not yielding any waters. How do I change the resolution cutoff for water picking to be 3.0 Angstroms? I tried adding "refinement.ordered_solvent.low_resolution=3.0" to my command line arguments and phenix is reading this, but the refinement crashes about 15 seconds in with the message: ================== Extract refinement strategy and selections ================= Sorry: Selection string 'water' results in empty selection (selects no atoms). Thanks for your help! -Sam

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Ligandfit problems with ligand geometry
by Kendall Nettles 10 Sep '09

10 Sep '09

I just tried ligandfit for the first time and it did not maintain proper geometry of the ligand. There were problems with both bond lengths and planarity. Is there a way to specify a .cif file? The ligand pdb was generated with PROGRD2, and I have had good success refining a structure that contains a very close analog with phenix.refine. Kendall Nettles

2 1

Phaser and anisotropy question
by Peter Grey 10 Sep '09

10 Sep '09

Dear Phenix users, I have a very anisotropic data as phaser reports anisotropic deltaB = 60.2. I would be grateful for advice of several issues. 1.Could you please tell me if phaser map coefficients FWT,PHWT take into account the anisotropic scaling ? 2.This means that these coefficients will be different from those calculated from a partial model in sigmaa because sigmaa has no anisotropic scaling (and no bulk solvent correction) ? 3.In the case of such severe anisotropy can the scaling diminish too strongly the well measured high resolution reflections ? If so should I calculate the coefficients my self by sigmaa and not use pahser mtz output or is there a better solution ? Many thanks in advance for sharing your thoughts and experience, Peter.

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Re: [phenixbb] Phenix crashes
by Katya Heldwein 10 Sep '09

10 Sep '09

Nat, 1.4-160 works just fine. Thank you. Katya Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Phenix crashes (Katya Heldwein) > 2. Re: Phenix crashes (sbiswas2(a)ncsu.edu) > 3. Re: Phenix crashes (Nathaniel Echols) > 4. Re: Phenix crashes (Nathaniel Echols) > 5. specifying column labels for input MTZ file > (Tirumala Kumar Chowdary) > 6. Re: specifying column labels for input MTZ file > (Schubert, Carsten [PRDUS]) > 7. Re: specifying column labels for input MTZ file (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 09 Sep 2009 12:02:36 -0400 > From: Katya Heldwein <Katya.Heldwein(a)tufts.edu> > Subject: [phenixbb] Phenix crashes > To: phenixbb(a)phenix-online.org > Message-ID: <20090909120236.c2mlsf9lww00kwsk(a)webmail.tufts.edu> > Content-Type: text/plain; charset=ISO-8859-1; format="flowed" > > Hi, > > I am running phenix-1.4-159 on an Intel Mac. I get the following error: > > Bus error (Python call stack above) > This crash may be due to a problem in any imported > Python module, including modules which are not part > of the cctbx project. To disable the traps leading > to this message, define these environment variables > (e.g. assign the value 1): > BOOST_ADAPTBX_FPE_DEFAULT > BOOST_ADAPTBX_SIGNALS_DEFAULT > This will NOT solve the problem, just mask it, but > may allow you to proceed in case it is not critical. > > If I fix it by > > setenv BOOST_ADAPTBX_FPE_DEFAULT 1 > > I still get the same error. > > If I also do > > setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 > > I don't get the error but phenix crashes nonetheless. > > How do I get around this problem? > > Thanks, > > Katya > > > > > ------------------------------ > > Message: 2 > Date: Wed, 9 Sep 2009 12:17:36 -0400 (EDT) > From: sbiswas2(a)ncsu.edu > Subject: Re: [phenixbb] Phenix crashes > To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> > Message-ID: <1476.152.1.132.71.1252513056.squirrel(a)webmail.ncsu.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hi, > This looks like a version problem, try installing the latest nightly builds. > Shya > > > >> Hi, >> >> I am running phenix-1.4-159 on an Intel Mac. I get the following error: >> >> Bus error (Python call stack above) >> This crash may be due to a problem in any imported >> Python module, including modules which are not part >> of the cctbx project. To disable the traps leading >> to this message, define these environment variables >> (e.g. assign the value 1): >> BOOST_ADAPTBX_FPE_DEFAULT >> BOOST_ADAPTBX_SIGNALS_DEFAULT >> This will NOT solve the problem, just mask it, but >> may allow you to proceed in case it is not critical. >> >> If I fix it by >> >> setenv BOOST_ADAPTBX_FPE_DEFAULT 1 >> >> I still get the same error. >> >> If I also do >> >> setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 >> >> I don't get the error but phenix crashes nonetheless. >> >> How do I get around this problem? >> >> Thanks, >> >> Katya >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> > > > > ------------------------------ > > Message: 3 > Date: Wed, 9 Sep 2009 09:37:50 -0700 > From: Nathaniel Echols <NEchols(a)lbl.gov> > Subject: Re: [phenixbb] Phenix crashes > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <2C512891-F9F0-40FB-AC0A-FA8C810F65AF(a)lbl.gov> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 9, 2009, at 9:02 AM, Katya Heldwein wrote: > >> I am running phenix-1.4-159 on an Intel Mac. I get the following >> error: >> Bus error (Python call stack above) >> >> If I fix it by >> setenv BOOST_ADAPTBX_FPE_DEFAULT 1 >> I still get the same error. >> If I also do >> >> setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 >> >> I don't get the error but phenix crashes nonetheless. >> >> How do I get around this problem? >> > > > Which programs are you running, and did you see a stack trace before > the error message? I just noticed the same thing running > phenix.refine from the same installer on my Mac, so it is probably an > undiagnosed bug. > > ------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 9 Sep 2009 09:46:24 -0700 > From: Nathaniel Echols <NEchols(a)lbl.gov> > Subject: Re: [phenixbb] Phenix crashes > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <6207C287-B0BB-4A7B-AD8E-2290222334FE(a)lbl.gov> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 9, 2009, at 9:17 AM, sbiswas2(a)ncsu.edu wrote: > >> Hi, >> This looks like a version problem, try installing the latest nightly >> builds. >> Shya >> > > > Actually, 1.4-159 was the latest build until ten minutes ago, but I > just checked 1.4-160 and it does not appear to have this problem, so > it's now ready to download. Sorry for the trouble. > > -Nat > > ------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > > > ------------------------------ > > Message: 5 > Date: Wed, 09 Sep 2009 14:10:27 -0400 > From: Tirumala Kumar Chowdary <Tirumala.Chowdary(a)tufts.edu> > Subject: [phenixbb] specifying column labels for input MTZ file > To: phenixbb(a)phenix-online.org > Message-ID: <20090909141027.belblmob7s4s440w(a)webmail.tufts.edu> > Content-Type: text/plain; charset=ISO-8859-1; format="flowed" > > Hi, > > I am trying to run phenix.refine with a sharp output MTZ file (column > labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD > HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). > > Phenix.refine stopped at > > 'Multiple equally suitable arrays of observed xray data found. > > Possible choices: > sharp_sad_se_eden.mtz:FP,SIGFP > sharp_sad_se_eden.mtz:Fav,SIGFav > > Please use refinement.input.xray_data.labels' > > Can someone tell me on how to use this > 'refinement.input.xray_data.labels' and how to specify which column > labels to use. There is nothing written in the documentation about it. > > Thanks > Tirumal > > > > > > > ------------------------------ > > Message: 6 > Date: Wed, 9 Sep 2009 14:22:40 -0400 > From: "Schubert, Carsten [PRDUS]" <CSCHUBER(a)its.jnj.com> > Subject: Re: [phenixbb] specifying column labels for input MTZ file > To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> > Message-ID: > <204D6E1BD9ACEA40B3F76FE9C125528F035DE9FF(a)JNJUSSHGMS01.na.jnj.com> > Content-Type: text/plain; charset="us-ascii" > > Tirumal: > > refinement.input.xray_data.labels="FP,SIGFP" > > should do the trick. > > Cheers, > > Carsten > > > >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org [mailto:phenixbb- >> bounces(a)phenix-online.org] On Behalf Of Tirumala Kumar Chowdary >> Sent: Wednesday, September 09, 2009 2:10 PM >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] specifying column labels for input MTZ file >> >> Hi, >> >> I am trying to run phenix.refine with a sharp output MTZ file (column >> labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC >> > HLD > >> HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). >> >> Phenix.refine stopped at >> >> 'Multiple equally suitable arrays of observed xray data found. >> >> Possible choices: >> sharp_sad_se_eden.mtz:FP,SIGFP >> sharp_sad_se_eden.mtz:Fav,SIGFav >> >> Please use refinement.input.xray_data.labels' >> >> Can someone tell me on how to use this >> 'refinement.input.xray_data.labels' and how to specify which column >> labels to use. There is nothing written in the documentation about it. >> >> Thanks >> Tirumal >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > > > ------------------------------ > > Message: 7 > Date: Wed, 09 Sep 2009 11:24:46 -0700 > From: Pavel Afonine <PAfonine(a)lbl.gov> > Subject: Re: [phenixbb] specifying column labels for input MTZ file > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Cc: Tirumala.Chowdary(a)tufts.edu > Message-ID: <4AA7F2EE.6080106(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Tirumala, > > I agree, you are not the first who confused by this and an example right > in the message would help. > > First, your MTZ file contains the following data: (FP,SIGFP) and > (Fav,SIGFav) and it is your choice to select the one that you want to > use in refinement. > > Second, once decided on the data - for example it is FP, then just add > to your command line this: > > refinement.input.xray_data.labels=FP > > or, which is the same > > xray_data.labels="FP,SIGFP" > > Pavel. > > > > On 9/9/09 11:10 AM, Tirumala Kumar Chowdary wrote: > >> Hi, >> >> I am trying to run phenix.refine with a sharp output MTZ file (column >> labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD >> HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). >> >> Phenix.refine stopped at >> >> 'Multiple equally suitable arrays of observed xray data found. >> >> Possible choices: >> sharp_sad_se_eden.mtz:FP,SIGFP >> sharp_sad_se_eden.mtz:Fav,SIGFav >> >> Please use refinement.input.xray_data.labels' >> >> Can someone tell me on how to use this >> 'refinement.input.xray_data.labels' and how to specify which column >> labels to use. There is nothing written in the documentation about it. >> >> Thanks >> Tirumal >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 46, Issue 14 > **************************************** >

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run autosol with rough phases from shelx?
by Francis E Reyes 09 Sep '09

09 Sep '09

Hi all Is it possible to input the phs file from a shelx run into an autosol run for some phase improvement with solve/resolve?? I tried putting in the HA sites but then the resultant map is worse. Also what are acceptable skews for low resolution phasing (worse than 4A) ? I understand the docs say 0.1 but does that also apply for low res? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Phenix crashes
by Katya Heldwein 09 Sep '09

09 Sep '09

Hi, I am running phenix-1.4-159 on an Intel Mac. I get the following error: Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. If I fix it by setenv BOOST_ADAPTBX_FPE_DEFAULT 1 I still get the same error. If I also do setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 I don't get the error but phenix crashes nonetheless. How do I get around this problem? Thanks, Katya

3 3

question about pick water in autobuild
by crystallogrphy 08 Sep '09

08 Sep '09

Hi, I am building a model against a 2.1A data set using phenix.autobuild. Right now Rfree is about 35%. I do not want to pick water in this stage because I see denisty at N-terminal of my model which need to build more residues. However, the program still picks water even after I say 'place_waters=False'. Does anyone know why? phenix.autobuild data=exptl_fobs_phases_freeR_flags.mtz model=AutoBuild_run_4_/overall_best-090905a.pdb seq_file=../ztb-sd.seq refinement.place_waters=False refinement.refine_with_ncs=True nproc=2

5 6

RuntimeError
by Young-Jin Cho 08 Sep '09

08 Sep '09

Hi everyone, while I was running phenix, I got the following error message. Could some one give me any tips to deal with such this problem? Thanks in advace, YoungJin Traceback (most recent call last): File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/command_line/refine.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 227, in __init__ self.pdb_file_names) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 876, in process_pdb_files raw_records = raw_records) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 907, in _process_pdb_file log = self.log) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2912, in __init__ log=log) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1962, in __init__ self.site_symmetry_table().special_position_indices() File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2217, in site_symmetry_table sites_cart=self.sites_cart) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/cctbx/crystal/__init__.py", line 394, in site_symmetry_table assert_min_distance_sym_equiv=self.assert_min_distance_sym_equiv()) RuntimeError: cctbx Error: site_symmetry: min_distance_sym_equiv too large. --

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Re: [phenixbb] question about pick water in autobuild
by Thomas C. Terwilliger 08 Sep '09

08 Sep '09

Hi Qun, With your command you need to add one more keyword to get rid of all the waters: place_waters_in_combine=False I'm sorry that doesn't happen automatically if you say place_waters=False ...I will make that happen in the future. Note however that these waters should not interfere with building...as waters are always deleted prior to building model. I note also that your command does not add new residues; it only adjusts the ones that are there. To build new model add: rebuild_in_place=False All the best, -Tom T >> Hi, >> >> from what you explain, the main issue I see here is that the model building program does not treat water simply as density peaks, and so removes them (waters) if necessary to build a protein chain instead. >> >> Otherwise, it's probably a good idea in general to fill in all unmodeled >> places with some placeholders like water, or probably isolated N atoms would work even better (if I recall correctly). >> >> Pavel. >> >> >> On 9/7/09 6:18 AM, crystallogrphy wrote: >>> Hi, Pavel: >>> The problem here is that autobuild placed waters into the densities where they are the N-terminal residues. Without the waters here, autobuild will build residues, not waters, to decrease R and Rfree with less model bias. Now with water picking, autobuild does not build more residues, just water. >>> I still do not know why 'place_waters=False' cannot work. Tom has not given me the answer yet. >>> On Mon, Sep 7, 2009 at 1:45 AM, Pavel Afonine <PAfonine(a)lbl.gov <mailto:[email protected]>> wrote: >>> Hi, >>> I hope Tom gives you the answer about how to stop water picking in autobuild. >>> From my side, I'm wondering why it bothers you (I'm not saying that not working option is good)? Why don't you consider those waters as a tool for improving your map? You are free to remove any of them them later on. This can be viewed as a prototype of what ARP/wARP does, or other "density growing" techniques... In your case you just temporarily place waters where the model is still absent, and when you build those missing places just consider waters as density peaks (I hope model building programs assume waters as just density peaks and remove waters if they are on the macromolecule's way). On the other hand, model >>> incompleteness may make the map ugly even for relatively well defined places. >>> Pavel. >>> On 9/6/09 7:38 AM, crystallogrphy wrote: >>>> Hi, >>>> I am building a model against a 2.1A data set using >>>> phenix.autobuild. Right now Rfree is about 35%. I do not want to pick water in this stage because I see denisty at N-terminal of my model which need to build more residues. However, the program still picks water even after I say 'place_waters=False'. Does anyone know why? >>>> phenix.autobuild data=exptl_fobs_phases_freeR_flags.mtz >>>> model=AutoBuild_run_4_/overall_best-090905a.pdb >>>> seq_file=../ztb-sd.seq refinement.place_waters=False >>>> refinement.refine_with_ncs=True nproc=2 >>>> ------------------------------------------------------------------------ _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org <mailto:[email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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about kick map generation
by crystallogrphy 04 Sep '09

04 Sep '09

Hi, I am generating a averaged kick maps with the following script. According to the script, there should be both kick map and normal 2fofc maps. However, there is only one map files created. I am not sure it is kick map or routine 2fofc map. Does anyone knows? electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_kick" mtz_label_phases = "PHFOFCWT_kick" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_no_fill" mtz_label_phases = "PHFOFCWT_no_fill" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } anomalous_difference_map { mtz_label_amplitudes = "ANOM" mtz_label_phases = "PHANOM" } grid_resolution_factor = 0.25 region = *selection cell atom_selection = None atom_selection_buffer = 3 apply_sigma_scaling = True apply_volume_scaling = False }

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assertion error with autobuild (phenix 1.4.3)
by Jan Stout 04 Sep '09

04 Sep '09

Dear, I am trying to run the Autobuild Wizard to make a iterative-build omit map. I get the following errors after running Autobuild using the input file autobuild.eff generated by the wizard itself. I am working with phenix 1.4.3. Any input will be greatly appreciated. Many thanks, Jan Stout Traceback (most recent call last): File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/command_line/autobuild.py", line 339, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 598, in __init__ self.RunWizard() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 973, in RunWizard self.runWizard.run() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 230, in run self.Wizard.Run(info='script') File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/AutoBaseExtend.py", line 726, in Run ok=self.CollectInputs()# raises AssertionError on failure File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/AutoBaseExtend.py", line 1790, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/wizards/AutoBuild.py", line 1074, in finish_AutoBuild_start all_files_ok=self.finish_Build_start() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/BuildBase.py", line 382, in finish_Build_start all_files_ok=self.Build_finish_up_start() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/BuildBase.py", line 508, in Build_finish_up_start str(self.Facts['input_data_file'])+"'") File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/UserMethods.py", line 84, in Error raise AssertionError,self.ErrorLine AssertionError: Sorry, cannot find the input_data_file ''

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question about phenix.refine
by crystallogrphy 03 Sep '09

03 Sep '09

Hi, I want to use phenix to refine a model right after autobuild with the following script: phenix.refine xray_data.file_name=exptl_fobs_phases_freeR_flags.mtz overall_best-090903a.pdb strategy=rigid_body+individual_sites simulated_annealing=true simulated_annealing.start_temperature=8000 sites.rigid_body="chain A" sites.rigid_body="chain B" However, the program says " F-obs: exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP If previously used R-free flags are available run this command again with the name of the file containing the original flags as an additional input. If the structure was never refined before, or if the original R-free flags are unrecoverable, run this command again with the additional definition: refinement.input.xray_data.r_free_flags.generate=True when I use phenix.mtz.dump exptl_fobs_phases_freeR_flags.mtz, it indicates that it has FreeR_flag=1. Can anyone tell me why there is FreeR_flag in my data, while the refinement program does not recognize it? label #valid %valid min max type H 35619 100.00% 0.00 22.00 H: index h,k,l K 35619 100.00% 0.00 45.00 H: index h,k,l L 35619 100.00% -33.00 33.00 H: index h,k,l FP 35619 100.00% 0.00 114.22 F: amplitude SIGFP 35619 100.00% 0.15 6.13 Q: standard deviation PHIM 35619 100.00% 0.00 0.00 P: phase angle in degrees FOMM 35619 100.00% 0.00 0.00 W: weight (of some sort) FreeR_flag 35619 100.00% 0.00 1.00 I: integer FC 35619 100.00% 0.00 0.00 F: amplitude

2 1

target omit map
by Susan Tsutakawa 03 Sep '09

03 Sep '09

I am trying to generate a simulated annealing omit map of a Mg-water cluster in the active site of my protein but when I run the SA omit map, I can only see the Mg when I use the Mgwater cluster as the target pdb. When I was building the model which did not have the metal present (phases solved by MR), I observed this Mg-water cluster in the Fo-Fc maps. Geometry and distance were ideal, etc. Now that I'm at the final stages of refinement, I would like to do a SA omit map as a figure for the paper. However, if I goto the lowest sigma, I only see the Mg. I'm using coot with the weights included to view the SA omit maps. I noticed that there is very little noise at the lowest sigma and so I'm wondering if the 0 sigma is truly 0 sigma and any suggestions on what to do. Thank you in advance. Sincerely, Susan

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reflection file utils : .cif?
by Bryan W. Lepore 03 Sep '09

03 Sep '09

[ phenix 1.4r3 cctbx tag: 2008_12_07_1353 intel-linux-2.6 redhat-e4.7 ] i obtained a recent .cif from the PDB, then run : phenix.reflection_file_converter --mtz=output.mtz test.cif file_name: test.cif file_type: None No reflection data found in input file. .... not sure where to go from here (a clip of the file is below, hope not too much) - i know i can run ccp4:cif2mtz, but are .cif part of phenix.reflection_file_converter? -bryan (sample of test.cif): data_testsf # _diffrn_radiation.id 1 _diffrn_radiation.pdbx_wavelength 1.00600 # _audit.revision_id 1_0 _audit.creation_date 2009-07-07 _audit.update_record 'Initial release' # _symmetry.Int_Tables_number 1 _symmetry.space_group_name_H-M 'P 1' # _cell.length_a 79.6610 _cell.length_b 104.1490 _cell.length_c 154.0250 _cell.angle_alpha 81.9570 _cell.angle_beta 75.9250 _cell.angle_gamma 73.7280 # _reflns.d_resolution_high 2.967 _reflns.d_resolution_low 46.392 _reflns.limit_h_max 26 _reflns.limit_h_min -25 _reflns.limit_k_max 34 _reflns.limit_k_min -34 _reflns.limit_l_max 51 _reflns.limit_l_min 0 _reflns.number_all 93210 _reflns.number_obs 85990 # loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.status _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au 1 1 1 o -25 -16 1 218.4 77.9 1 1 1 o -25 -15 1 250.7 87.9 1 1 1 o -25 -15 2 217.9 78.8 (... etc... here is a free set hkl :) 1 1 1 f -25 -7 3 315.6 89.7 (... etc... until the end :) #END OF REFLECTIONS

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Custom Planar Restraints
by cheung＠lmb.uni-muenchen.de 03 Sep '09

03 Sep '09

Hi all - is it possible to specify custom planar restraints in phenix.refine? I'm refining a 3.8A protein-dna complex and although i've set hydrogen bonding restraints between base pairs, they still become very twisted and buckled after refinement. Alan

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question about autobuild
by crystallogrphy 03 Sep '09

03 Sep '09

Hi, I have used phenix.automr followed by phenix.autobuild to build a 264 residue model against my 2.1A resolution data set. The first run of autobuild gives me about 180 residues built. I have adjusted the model according to the denity. The N-terminal of the model has OK density to add more residues to the model. Can phenix.autobuild has some command to just put more residues to the N-terminal of my current model according to the density, so that the cost of CPU time will be much less than rerun the job completely? Thanks!

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Chain id of water is not reading by coot
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, I have 7 chains in my pdb file. When I am reading the pdb file in COOT, for some reason the chain id(W) of water is not coming in the list. I clicked on 'draw' and then 'go to atom'. I can see all other chains but not W. I created water in PHENIX Is there any wrong in my pdb? HETATM 7562 O HOH W 542 -9.043 -2.133 -12.633 1.00 34.55 W O HETATM 7563 O HOH W 543 -22.004 8.228 -21.695 1.00 34.55 W O HETATM 7564 O HOH W 544 5.926 38.977 -11.538 1.00 34.55 W O HETATM 7565 O HOH W 545 -31.162 5.813 -31.403 1.00 34.55 W O Raja

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Improving picture quality of ED map in PYMOL
by Raja Dey 01 Sep '09

01 Sep '09

Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja

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Source for Nightlys Location?
by Andrew Ring 01 Sep '09

01 Sep '09

Is it possible to get a source distribution for the nightlys? If so, where is it located? I can only finding the builds on the nightlys downloads page. For my systems and uses, the --openmp switch on version 1.4-3 has given encouraging results and I would like to investigate with something newer. -- =================================== Andrew Ring System Administrator Kuriyan Laboratory http://jkweb.qb3.berkeley.edu/ Doudna Laboratory http://rna.berkeley.edu/ University of California, Berkeley Office: 542 Stanley Hall Shipping: 176 Stanley Hall, QB3 Berkeley, CA 94720-3220 tel: (510) 643 0166 fax: (510) 643 2352 ====================================

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R-work is too low
by Sam Stampfer 01 Sep '09

01 Sep '09

Hi, I'm refining a 2.88 Angstrom structure and am getting a difference of greater than 6% between the R-work and R-free. The best result (I think) is what I have from minimization alone: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2424, R-free = 0.3174 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2411, R-free = 0.3176 The results from simulated annealing are the following: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2454, R-free = 0.3322 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2403, R-free = 0.3333 I have also done the refinement with ncs but ncs is probably not appropriate for my structure. The final R-free ends up being higher (though the difference between R-free and R-work ends up being 6-7%) My PI (who is on vacation until next week) said that it was a problem if R-work was more than 0.06 lower than R-free. Any recommendations for me? Is it possible to reduce this difference? Is it worth it to rebuild the refined pdb if the R-work is this different from the R-free? My refinement script is: phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \ output.prefix=results/ss46_rebuilt_sa \ strategy=individual_sites+group_adp cif_link.params nag-nag.cif \ twin_law="h,-h-k,-l" \ simulated_annealing=true (the cif_link.params and nag-nag.cif files are made to handle the N-glycosylation sites, I think). Thanks for your help! -Sam

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error TLS refinement
by Marjolein Thunnissen 01 Sep '09

01 Sep '09

I'm trying to finish refining a structure that has been almost refined completely about a year ago with an older version of Phenix.refine. When I start TLS refinement I get the following error message: RuntimeError : mean_weighted() argument is an empty array Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 259, in OnExcept raise event.data RuntimeError: mean_weighted() argument is an empty array I do not get this error when refining without TLS, only when I switch it on. The program advises me to post the error here so... Thanks Marjolein ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)46-22 24584 Associate Professor Fax +46-(0)46-22 24692 Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations for macromolecular crystallography ________________________________________________________________________

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Specifying the number of processors to run phenix with
by Sam Stampfer 31 Aug '09

31 Aug '09

Hi- anyone know how to specify the number of processors to run phenix under in linux? Or how to tell what the default is? I'm running linux (fedora) with 4 processors and can't tell whether phenix is using all of them or not. I do the refinement with .csh files and tried doing "myfile.csh --nproc=4". The file ran but no faster- I can't tell if it is using 4 by default or if that's the incorrect command to specify the use of 4 processors. Thanks for your help! -Sam

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Best first map for RESOLVE after MR
by Peter Grey 31 Aug '09

31 Aug '09

Hello all, I try to solve the structure of a big complex at rather low resolution. I have a molecular replacement solution with a partial model from Phaser. I would like to use RESOLVE for density modification. I ask for your advice regarding the first map that should be the input into RESOLVE. Should it be the 2mFo-DFc map directly from Phaser or would it be better to do rigid body refinement in phenix.refine and use the bulk solvent corrected 2mFo-DFc map ? Many thanks in advance for your suggestions, Peter.

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