- phenixbb - phenix-online.org

autobuild wizard question
by Jeff Habel 17 Aug '07

17 Aug '07

I'm a new PHENIX user and having trouble with the Autobuild wizard. The structure has 2 molecules in the asymmetric unit and I am trying to build a small portion (286-297) of both chains. I have tried building both at the same time and trying just chain A but always receive the error about needing 2 amino acids on either end for anchoring the build. Every time I alter the build range (284... 299... 282... 301... etc) the error persists. Any suggestions would be appreciated. Thanks, -Jeff **************************************** Jeff Habel PhD Scripps Florida Drug Discovery 5353 Parkside Dr, RF-1 Rm 102 Jupiter, FL 33458 Phone: 561-799-8849 Fax: 561-799-8957 Email: jhabel(a)scripps.edu *****************************************

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Re: [phenixbb] TLS refinement
by Pavel Afonine 17 Aug '07

17 Aug '07

Hi John, > I was wondering if there is an easy way to take the output from TLSmd > and input the definitions into phenix.refine. Unfortunately, I do not know since it never happened to me to use it. It is our long term plan to implement our own automatic TLS domains identification option. > If any one has an example file of a phenix TLS file with multiple TLS > definitions per chain I would love to have it (The manual just gives > an example of TLS definitions of one per chain, but I am getting > confused on how to define mutlitple). I'm loading two files at the web address below: one with TLS selections for multiple groups, another one is the PDB file with refined model and TLS records in its header. This is actually the most complex selection for TLS groups I ever used -:) http://cci.lbl.gov/~afonine/tls_selections/ Please let me know if you have any more questions. Pavel.

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TLS refinement
by John Bruning 17 Aug '07

17 Aug '07

Hi, I was wondering if there is an easy way to take the output from TLSmd and input the definitions into phenix.refine. If any one has an example file of a phenix TLS file with multiple TLS definitions per chain I would love to have it (The manual just gives an example of TLS definitions of one per chain, but I am getting confused on how to define mutlitple). Thanks, John Bruning

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Re: [phenixbb] Question about precedence of command line parameters vs. .def file
by Ralf W. Grosse-Kunstleve 15 Aug '07

15 Aug '07

Hi Carsten, > I see how the loading of both pdb files can be a desired feature, but I > also recall reading somewhere that command line params take precedence > over .def files, which in turn takes precedence over defaults. There > seems to be some deviation from that philosophy. Each parameter has a bunch of associated attributes to control the behavior. The attribute that causes trouble here is .multiple=True. It means that you can specify multiple values. Values accumulate in the order given. .multiple=True is used in many places and in general this feature works well, but in the case of the pdb file name it sometimes causes confusion. Unfortunately I don't see an obvious way around this. It would be possible to support something like pdb.file_name==your.pdb, where == means discard all accumulated values and start over with the new value, but that wouldn't be very intuitive. Or we'd have to stop supporting reading of multiple pdb files. I wonder if you could achieve your goals with a different approach. The idea is not to use the .def files produced by phenix.refine. I'm guessing you're doing this because they contain all your accumulated customizations defined via the command line. Could you organize your workflow to accumulate the customizations in a separate file, then pass that file as another argument? E.g.: Content of "params" file: refinement.main.macro_cycles=5 refinement.main.high_resolution=3 phenix.refine my.pdb params > This also would help future automation we are implementing, because > it would eliminate the need to read and parse an existing .def. file. Parsing and rewriting a .def file is very easy from Python. If you have phenix, you also have both Python and a parameter file parser and writer. The "phil" parser/writer is documented in this newsletter article: http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf I could help you getting started if that's an interesting alternative. If you can think of a more intuitive way of handling the interaction of parameters with multiple values and command-line parameters, please let me know! Ralf

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Question about precedence of command line parameters vs. .def file
by Schubert, Carsten [PRDUS] 15 Aug '07

15 Aug '07

Hi, I have a question / request about parameters defined on the command line vs. defined in the .def file are handled. Specifically the input.pdb.file_name parameter. I noticed that if I have already a input.pdb.file_name defined in the .def file and call phenix.refine with another pdb file, both files are loaded. If both pdb files represent the same protein in different stages of refinement that obviously causes the job to fail due to close non-bonding interactions. I see how the loading of both pdb files can be a desired feature, but I also recall reading somewhere that command line params take precedence over .def files, which in turn takes precedence over defaults. There seems to be some deviation from that philosophy. For me this is more a work-flow issue (which becomes important if one does to many structures per day ...) than a bug. I'd really like to minimize the time spend on editing the def file and just define new job parameters from the command line and have the def file fill in the missing bits. This also would help future automation we are implementing, because it would eliminate the need to read and parse an existing .def. file. There are ways around this but not as clean, but that is another matter .... Would it be possible to implement a switch which would check for duplicate parameters on the command line vs. .def file, give precedence to the command line and run the job like that? That way we would not break the existing scheme, which other people may have already grown accustomed too. Other suggestions are welcome too. Cheers, Carsten

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conversion from h3 to r3 with phenix apps
by Green, Todd 15 Aug '07

15 Aug '07

Hello all, I have what i believe to be a rhombohedral crystal that has an insanely large cell with the hexagonal setting: 533.026 533.026 652.887 90.000 90.000 120.000 and a modestly large cell comparatively with the rhombohedral setting: 377 377 377 90 90 90 I should be able to easily reindex to the smaller cell in scalepack but for some reason i'm not getting it to work correctly. Rather than struggle further on a friday afternoon, i figured that i'd give a phenix app a try. i assume xtriage can do this, can someone point me in the correct direction? thanks in advance- Todd

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refinement questions
by Sudharsan Sridharan 11 Aug '07

11 Aug '07

Hi all, I'm starting to refine a structure using phenix.refine. Almost all my model residues have been built starting from a Sharp map. I've been trying phenix.refine with and without SA and getting bond angle rmsds of 1.0 -1.1 (2.5 A data, using mlhl targets; example below) (yet to add water and also trying water picking in phenix.refine). I'm wondering if this sounds low (I have read discussions on bond and angle rmsds). More importantly I'd like to know how to work with different parameters (weights etc) during refinement in phenix. Could you please point to what params are safe to manipulate. Thanks, Sid. REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.3637 r_free = 0.4003 bonds = 0.010 angles = 1.175 REMARK Final: r_work = 0.2607 r_free = 0.3236 bonds = 0.007 angles = 1.017 REMARK ************************************************************************

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Position for PSI Knowledgebase development
by Paul Adams 08 Aug '07

08 Aug '07

======================================================================= Lawrence Berkeley National Laboratory Software Developer II ======================================================================= Software Developer II Job ID: 20930 Division: Physical Biosciences Date Opened: 8/7/2007 Summary This position will be part of the Computational Crystallography Initiative at Lawrence Berkeley Lab and will be responsible for developing a web site to disseminate information about the Technologies developed by the NIH Protein Structure Initiative (PSI). This program funds the majority of structural genomics efforts within the US and is responsible for the development of many new technologies that are useful to macromolecular crystallographers. This technology resource is part of the larger PSI Knowledge Base that will provide an information portal for the scientific community. Duties Essential: Under general direction of the Principal Investigator: Develop and maintain web site documenting PSI developed technologies. Interact with PSI researchers to collect information about new technologies. Create a relational database to store crystallographic data. Install and maintain SVN repositories for the PSI community. Marginal: Perform routine analysis of crystallographic data. Maintain web site computing hardware and software. Other duties as assigned. Qualifications Essential: Experience with writing and maintaining HTML web pages. Knowledge of standard programming methods, and Python in a UNIX environment. Strong analytical and organizational skills. Ability to handle multiple tasks in parallel. Excellent interpersonal skills for working in a diverse team environment, ability to interact effectively with other scientists, and to address their needs in an effective and timely manner. Marginal: B.S. Degree or higher in biophysics, computer science, chemistry, electrical engineering, physics or related field preferred or equivalent experience, with demonstrated programming experience. Experience maintaining computing hardware and software. Experience with analysis of crystallographic data. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20930. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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ncs restraints weight
by Daniele de Sanctis 07 Aug '07

07 Aug '07

Dear all, i'm refining a low resolution structure (3.2A) with four molecules in the asymmetric unit. I saw that phenix.refine doesn't allow constraints, so i'd like to change the restraints weight but i can't find the right keyword... thanks for your help d -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartato 127 2781-901 Oeiras Portugal

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Re: [phenixbb] set_biso_to_wilson_b gone?
by Pavel Afonine 06 Aug '07

06 Aug '07

Hi Luca, > I've just noticed that in the last version of PHENIX (1.3b-d7) this is > not recognised anymore: > > refinement.modify_start_model.adp.set_biso_to_wilson_b = true > > is this intentional? I'm afraid, yes. There are some technical reasons for this. You still have at least two ways of doing this: 1) When running phenix.refine : % phenix.refine data.mtz model.pdb modify_start_model.adp.set_b_iso=xxx where xxx is Wilson B values (that you may get from previous phenix.refine runs; phenix.refine reports it). 2) We recently added a tool for PDB file(s) manipulations. Currently it is very simple but will grow based on needs and user's requests. For example, it can read in a model and for selected or all atoms: - modify ADP (randomize, shift, set to a value, scale, convert to/from iso(aniso)tropic); - modify sites (shake, apply rotation / translation); - modify occupancies; - remove selected atoms; - write out a PDB file with modified model. To get started type: phenix.pdbtools -h I'm attaching a copy of a quick manual for phenix.pdbtools (it will be a part of new updated PHENIX documentation). Pavel.

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Re: [phenixbb] Problematic dataset
by Peter Zwart 06 Aug '07

06 Aug '07

Hi Lucas, Your P21 just looks twinned. Have a look at the last section of the xtriage output: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 1.915 - <F>^2/<F^2> : 0.821 - <|E^2-1|> : 0.677 - <|L|>, <L^2>: 0.442, 0.267 Multivariate Z score L-test: 3.623 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | h,-k,-h-l | PM | 0.090 | 0.406 | 0.417 | 0.370 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 6.379 (correpsonding p value : 6.273e-01) The largest off-origin peak in the Patterson function is 6.38% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are twin laws possible given the crystal symmetry, twinning could be the reason for the departure of the intensity statistics from normality. It might be worthwhile carrying out refinement with a twin specific target function. ------------------------------------------------------------------------------- You might have NCS parallel to the twin axis. If you run mmtbx.xtwin_map_utils on your P21 data, you get a mtzfile called obs_and_calc.mtz push that through xtriage (make sure to specify labels for observed and calculated data) to get the RvsR statistic. When you do that, please also provide the keyword 'perform=True' on the xtriage command line for my pleasure and send me the resulting log file. I guess the twin refinement will push the r values down a bit. Note that for futurte reference, xtriage produces a logfile as well, usually named logfile.log unless you ask it to be a different name. logfile.log contains some ccp4 style graphs you can view with loggraph (such as the L, NZ, Britton and H curves). If the above is too cryptic and you need more info, please let me know. HTH Peter Lucas Bleicher wrote: > Hi, Peter! > > I am sending the xtriage output for both space groups. > > So, the correct approach would be to use the MTZ > processed in P21 with the twin law from the xtriage > output from this MTZ file? > > Thanks in advance, > Lucas > > > Alertas do Yahoo! Mail em seu celular. Saiba mais em http://br.mobile.yahoo.com/mailalertas/ > ------------------------------------------------------------------------ > > ############################################################# > ## mmtbx.xtriage ## > ## ## > ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## > ## ## > ############################################################# > Date 2007-07-31 Time 16:43:49 BRT -0300 > > > ##-------------------------------------------## > ## WARNING: ## > ## Number of residues unspecified ## > ##-------------------------------------------## > > > Effective parameters: > scaling.input { > parameters { > asu_contents { > n_residues = None > n_bases = None > n_copies_per_asu = None > } > misc_twin_parameters { > missing_symmetry { > tanh_location = 0.08 > tanh_slope = 50 > } > twinning_with_ncs { > perform_analyses = False > n_bins = 7 > } > twin_test_cuts { > low_resolution = 10 > high_resolution = None > isigi_cut = 3 > completeness_cut = 0.85 > } > } > reporting { > verbose = 1 > log = "logfile.log" > ccp4_style_graphs = True > } > } > xray_data { > file_name = "LamNatP1High_scala1.mtz" > obs_labels = "MEAN_lnls,SIGIMEAN_lnls" > calc_labels = None > unit_cell = 52.16379929 64.59190369 108.2256012 89.99259949 89.99089813 \ > 66.10500336 > space_group = "P 1" > high_resolution = None > low_resolution = None > } > } > <scitbx_array_family_flex_ext.double object at 0xb5e96dac> > > > Symmetry, cell and reflection file content summary > > Miller array info: LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls > Observation type: xray.amplitude > Type of data: double, size=94082 > Type of sigmas: double, size=94082 > Number of Miller indices: 94082 > Anomalous flag: False > Unit cell: (52.1638, 64.5919, 108.226, 89.9926, 89.9909, 66.105) > Space group: P 1 (No. 1) > Systematic absences: 0 > Centric reflections: 0 > Resolution range: 26.0819 1.85 > Completeness in resolution range: 0.854134 > Completeness with d_max=infinity: 0.853839 > > ##----------------------------------------------------## > ## Basic statistics ## > ##----------------------------------------------------## > > > Matthews coefficient and Solvent content statistics > > Number of residues unknown, assuming 50% solvent content > > ---------------------------------------------------------------- > | Best guess : 1220 residues in the asu | > ---------------------------------------------------------------- > > > Completeness and data strength analyses > > The following table lists the completeness in various resolution > ranges, after applying a I/sigI cut. Miller indices for which > individual I/sigI values are larger than the value specified in > the top row of the table, are retained, while other intensities > are discarded. The resulting completeness profiles are an indication > of the strength of the data. > > ---------------------------------------------------------------------------------------- > | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | > ---------------------------------------------------------------------------------------- > | 26.08 - 4.55 | 97.0% | 96.3% | 95.5% | 93.5% | 87.3% | 80.3% | > | 4.55 - 3.62 | 96.5% | 96.1% | 95.4% | 93.8% | 87.8% | 81.2% | > | 3.62 - 3.16 | 95.7% | 94.5% | 93.2% | 89.4% | 78.1% | 66.3% | > | 3.16 - 2.87 | 93.1% | 90.7% | 87.1% | 79.1% | 60.8% | 44.5% | > | 2.87 - 2.67 | 88.4% | 84.0% | 78.5% | 66.7% | 44.0% | 27.9% | > | 2.67 - 2.51 | 85.5% | 78.6% | 71.1% | 57.7% | 32.6% | 17.9% | > | 2.51 - 2.38 | 82.4% | 74.1% | 65.3% | 49.3% | 24.8% | 12.2% | > | 2.38 - 2.28 | 81.6% | 72.3% | 62.4% | 46.0% | 20.4% | 9.0% | > | 2.28 - 2.19 | 78.5% | 67.6% | 55.1% | 37.2% | 14.8% | 5.7% | > | 2.19 - 2.12 | 75.5% | 61.9% | 49.0% | 30.7% | 9.9% | 3.5% | > | 2.12 - 2.05 | 72.1% | 55.6% | 41.8% | 23.7% | 6.3% | 1.9% | > | 2.05 - 1.99 | 68.6% | 50.2% | 35.8% | 17.9% | 4.1% | 1.0% | > | 1.99 - 1.94 | 63.2% | 42.9% | 28.5% | 13.7% | 3.1% | 0.5% | > | 1.94 - 1.89 | 56.6% | 36.7% | 23.2% | 10.4% | 1.7% | 0.3% | > ---------------------------------------------------------------------------------------- > > The completeness of data for which I/sig(I)>3.00, exceeds 85% for > for resolution ranges lower than 2.87A. > The data is cut at this resolution for the potential twin tests > and intensity statistics. > > > Maximum likelihood isotropic Wilson scaling > ML estimate of overall B value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > 15.59 A**(-2) > Estimated -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > -2.45 > > > Maximum likelihood anisotropic Wilson scaling > ML estimate of overall B_cart value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > 15.61, 1.39, -1.33 > 11.40, 0.27 > 21.10 > Equivalent representation as U_cif: > 0.18, -0.04, -0.02 > 0.14, 0.00 > 0.27 > > ML estimate of -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > -2.45 > Correcting for anisotropy in the data > > Some basic intensity statistics follow. > > > > Low resolution completeness analyses > > The following table shows the completeness > of the data to 5 Angstrom. > unused: - 26.0822 [ 0/38 ] 0.000 > bin 1: 26.0822 - 10.5555 [528/541] 0.976 > bin 2: 10.5555 - 8.4726 [551/564] 0.977 > bin 3: 8.4726 - 7.4299 [530/547] 0.969 > bin 4: 7.4299 - 6.7636 [568/582] 0.976 > bin 5: 6.7636 - 6.2860 [525/540] 0.972 > bin 6: 6.2860 - 5.9200 [547/559] 0.979 > bin 7: 5.9200 - 5.6266 [530/546] 0.971 > bin 8: 5.6266 - 5.3839 [519/532] 0.976 > bin 9: 5.3839 - 5.1783 [568/584] 0.973 > bin 10: 5.1783 - 5.0009 [516/532] 0.970 > unused: 5.0009 - [ 0/0 ] > > > > Mean intensity analyses > Analyses of the mean intensity. > Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. > The following resolution shells are worrisome: > ------------------------------------------------ > | d_spacing | z_score | compl. | <Iobs>/<Iexp> | > ------------------------------------------------ > | 9.993 | 7.15 | 0.97 | 0.426 | > | 8.448 | 7.29 | 0.98 | 0.559 | > | 7.451 | 6.09 | 0.97 | 0.676 | > | 4.303 | 4.64 | 0.97 | 1.223 | > | 3.410 | 4.52 | 0.96 | 1.176 | > | 3.333 | 6.63 | 0.96 | 1.262 | > | 3.261 | 5.36 | 0.96 | 1.205 | > | 3.194 | 5.48 | 0.96 | 1.203 | > | 3.071 | 4.87 | 0.94 | 1.183 | > | 2.962 | 6.43 | 0.94 | 1.245 | > | 2.911 | 4.61 | 0.93 | 1.160 | > | 2.454 | 4.96 | 0.87 | 0.872 | > | 2.425 | 6.89 | 0.87 | 0.825 | > | 2.397 | 4.68 | 0.87 | 0.873 | > | 2.182 | 6.79 | 0.84 | 0.830 | > | 2.142 | 5.54 | 0.84 | 0.856 | > | 1.870 | 5.46 | 0.60 | 1.205 | > | 1.857 | 11.65 | 0.54 | 1.570 | > ------------------------------------------------ > > Possible reasons for the presence of the reported > unexpected low or elevated mean intensity in > a given resolution bin are : > - missing overloaded or weak reflections > - suboptimal data processing > - satelite (ice) crystals > - NCS > - translational pseudo symmetry (detected elsewhere) > - outliers (detected elsewhere) > - ice rings (detected elsewhere) > - other problems > Note that the presence of abnormalities > in a certain region of reciprocal space might > confuse the data validation algorithm throughout > a large region of reciprocal space, even though > the data is acceptable in those areas. > > > Possible outliers > Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 > > Acentric reflections: > > ----------------------------------------------------------------- > | d_space | H K L | |E| | p(wilson) | p(extreme) | > ----------------------------------------------------------------- > | 2.114 | -18, -9, 35 | 3.79 | 5.57e-07 | 5.08e-02 | > | 3.066 | -16, -8, 12 | 3.93 | 1.90e-07 | 1.77e-02 | > | 3.066 | 16, 8, 12 | 3.95 | 1.69e-07 | 1.57e-02 | > | 2.115 | 18, 9, 35 | 3.79 | 5.65e-07 | 5.15e-02 | > ----------------------------------------------------------------- > > p(wilson) : 1-(1-exp[-|E|^2]) > p(extreme) : 1-(1-exp[-|E|^2])^(n_acentrics) > p(wilson) is the probability that an E-value of the specified > value would be observed when it would selected at random from > the given data set. > p(extreme) is the probability that the largest |E| value is > larger or equal then the observed largest |E| value. > > Both measures can be used for outlier detection. p(extreme) > takes into account the size of the dataset. > > > Centric reflections: > > None > > > Ice ring related problems > > The following statistics were obtained from ice-ring > insensitive resolution ranges > mean bin z_score : 3.46 > ( rms deviation : 1.89 ) > mean bin completeness : 0.89 > ( rms deviation : 0.09 ) > > The following table shows the z-scores > and completeness in ice-ring sensitive areas. > Large z-scores and high completeness in these > resolution ranges might be a reason to re-assess > your data processsing if ice rings were present. > > ------------------------------------------------ > | d_spacing | z_score | compl. | Rel. Ice int. | > ------------------------------------------------ > | 3.897 | 0.51 | 0.97 | 1.000 | > | 3.669 | 1.87 | 0.97 | 0.750 | > | 3.441 | 4.52 | 0.96 | 0.530 | > | 2.671 | 3.84 | 0.89 | 0.170 | > | 2.249 | 3.61 | 0.87 | 0.390 | > | 2.072 | 3.23 | 0.82 | 0.300 | > | 1.948 | 0.62 | 0.76 | 0.040 | > | 1.918 | 0.44 | 0.73 | 0.180 | > | 1.883 | 5.46 | 0.60 | 0.030 | > ------------------------------------------------ > > Abnormalities in mean intensity or completeness at > resolution ranges with a relative ice ring intensity > lower then 0.10 will be ignored. > > No ice ring related problems detected. > If ice rings were present, the data does not look > worse at ice ring related d_spacings as compared > to the rest of the data set > > > > > Basic analyses completed > > ##----------------------------------------------------## > ## Twinning Analyses ## > ##----------------------------------------------------## > > > > Using data between 10.00 to 2.87 Angstrom. > > Determining possible twin laws. > > The following twin laws have been found: > > --------------------------------------------------------------------------------- > | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | > --------------------------------------------------------------------------------- > | PM | 2-fold | 0.009 | 0.010 | 0.000 | -h,-k,l | > | PM | 2-fold | 0.090 | 0.079 | 0.001 | -h,-h+k,-l | > | PM | 2-fold | 0.099 | 0.080 | 0.001 | h,h-k,-l | > --------------------------------------------------------------------------------- > M: Merohedral twin law > PM: Pseudomerohedral twin law > > 0 merohedral twin operators found > 3 pseudo-merohedral twin operators found > In total, 3 twin operator were found > > > Number of centrics : 0 > Number of acentrics : 27599 > > Largest patterson peak with length larger then 15 Angstrom > > Frac. coord. : 0.119 -0.276 -0.000 > Distance to origin : 16.337 > Height (origin=100) : 5.893 > p_value(height) : 7.365e-01 > > The reported p_value has the following meaning: > The probability that a peak of the specified height > or larger is found in a Patterson function of a > macro molecule that does not have any translational > pseudo symmetry is equal to 7.365e-01 > p_values smaller then 0.05 might indicate > weak translation pseudo symmetry, or the self vector of > a large anomalous scatterer such as Hg, whereas values > smaller then 1e-3 are a very strong indication for > the presence of translational pseudo symmetry. > > > > Wilson ratio and moments > > Acentric reflections > <I^2>/<I>^2 :1.932 (untwinned: 2.000; perfect twin 1.500) > <F>^2/<F^2> :0.820 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.678 (untwinned: 0.736; perfect twin 0.541) > > > > NZ test (0<=z<1) to detect twinning and possible translational NCS > > > ----------------------------------------------- > | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | > ----------------------------------------------- > | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | > | 0.1 | 0.046 | 0.095 | 0.000 | 0.248 | > | 0.2 | 0.127 | 0.181 | 0.000 | 0.345 | > | 0.3 | 0.210 | 0.259 | 0.000 | 0.419 | > | 0.4 | 0.287 | 0.330 | 0.000 | 0.474 | > | 0.5 | 0.361 | 0.394 | 0.000 | 0.520 | > | 0.6 | 0.427 | 0.451 | 0.000 | 0.561 | > | 0.7 | 0.486 | 0.503 | 0.000 | 0.597 | > | 0.8 | 0.544 | 0.551 | 0.000 | 0.629 | > | 0.9 | 0.597 | 0.593 | 0.000 | 0.657 | > | 1.0 | 0.643 | 0.632 | 0.000 | 0.683 | > ----------------------------------------------- > | Maximum deviation acentric : 0.055 | > | Maximum deviation centric : 0.683 | > | | > | <NZ(obs)-NZ(twinned)>_acentric : -0.024 | > | <NZ(obs)-NZ(twinned)>_centric : -0.467 | > ----------------------------------------------- > > > L test for acentric data > > using difference vectors (dh,dk,dl) of the form: > (2hp,2kp,2lp) > where hp, kp, and lp are random signed integers such that > 2 <= |dh| + |dk| + |dl| <= 8 > > Mean |L| :0.441 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.267 (untwinned: 0.333; perfect twin: 0.200) > > The distribution of |L| values indicates a twin fraction of > 0.08. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > > > --------------------------------------------- > Analysing possible twin law : -h,-k,l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.053 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.005 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.447 > Estimation of twin fraction via cum. dist. of H: 0.449 > > > > Britton analyses > > Extrapolation performed on 0.47 < alpha < 0.495 > Estimated twin fraction: 0.442 > Correlation: 0.9953 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.054 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.004 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.415 > > > --------------------------------------------- > Analysing possible twin law : -h,-h+k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.093 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.015 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.407 > Estimation of twin fraction via cum. dist. of H: 0.407 > > > > Britton analyses > > Extrapolation performed on 0.44 < alpha < 0.495 > Estimated twin fraction: 0.399 > Correlation: 0.9959 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.093 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.011 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.361 > > > --------------------------------------------- > Analysing possible twin law : h,h-k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.085 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.013 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.415 > Estimation of twin fraction via cum. dist. of H: 0.417 > > > > Britton analyses > > Extrapolation performed on 0.46 < alpha < 0.495 > Estimated twin fraction: 0.411 > Correlation: 0.9961 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.086 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.009 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.350 > > > > Exploring higher metric symmetry > > The point group of data as dictated by the space group is P 1 > the point group in the niggli setting is P 1 > The point group of the lattice is Hall: C 2 2 (x+y,2*y,z) > A summary of R values for various possible point groups follow. > > ----------------------------------------------------------------------------------------------- > | Point group | mean R_used | max R_used | mean R_unused | min R_unused | choice | > ----------------------------------------------------------------------------------------------- > | Hall: C 2y (x-y,2*x,z) | 0.086 | 0.086 | 0.054 | 0.054 | | > | P 1 | None | None | 0.070 | 0.054 | | > | Hall: C 2y (x+y,2*y,z) | 0.093 | 0.093 | 0.054 | 0.054 | | > | Hall: C 2 2 (x+y,2*y,z) | 0.070 | 0.086 | None | None | | > | P 1 1 2 | 0.054 | 0.054 | 0.093 | 0.093 | <--- | > ----------------------------------------------------------------------------------------------- > > R_used: mean and maximum R value for symmetry operators *used* in this point group > R_unused: mean and minimum R value for symmetry operators *not used* in this point group > The likely point group of the data is: P 1 1 2 > > Possible space groups in this point groups are: > Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90) > Space group: P 1 2 1 (No. 3) > > Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90) > Space group: P 1 21 1 (No. 4) > > Note that this analyses does not take into account the effects of twinning. > If the data is (allmost) perfectly twinned, the symmetry will appear to be > higher than it actually is. > > > > > > ------------------------------------------------------------------------------- > Twinning and intensity statistics summary (acentric data): > > Statistics independent of twin laws > - <I^2>/<I>^2 : 1.932 > - <F>^2/<F^2> : 0.820 > - <|E^2-1|> : 0.678 > - <|L|>, <L^2>: 0.441, 0.267 > Multivariate Z score L-test: 3.807 > The multivariate Z score is a quality measure of the given > spread in intensities. Good to reasonable data is expected > to have a Z score lower than 3.5. > Large values can indicate twinning, but small values do not > neccesarily exclude it. > > > Statistics depending on twin laws > ------------------------------------------------------------------- > | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | > ------------------------------------------------------------------- > | -h,-k,l | PM | 0.054 | 0.442 | 0.449 | 0.415 | > | -h,-h+k,-l | PM | 0.093 | 0.399 | 0.407 | 0.361 | > | h,h-k,-l | PM | 0.086 | 0.411 | 0.417 | 0.350 | > ------------------------------------------------------------------- > > Patterson analyses > - Largest peak height : 5.893 > (correpsonding p value : 7.365e-01) > > > The largest off-origin peak in the Patterson function is 5.89% of the > height of the origin peak. No significant pseudotranslation is detected. > > The results of the L-test indicate that the intensity statistics > are significantly different then is expected from good to reasonable, > untwinned data. > As there are twin laws possible given the crystal symmetry, twinning could > be the reason for the departure of the intensity statistics from normality. > It might be worthwhile carrying refinement with a twin specific target function. > > Note that the symmetry of the intensities suggest that the assumed space group > is too low. As twinning is however suspected, it is not immediuatly clear if this > is the case. Carefull reprocessing and (twin)refinement for all cases might resolve > this question. > > -------------------------------------------------------------------------------

1 0

R, Rfree, and wxu_scale
by Jianghai Zhu 05 Aug '07

05 Aug '07

Hi, Just finished a round of refinement. Rfree went up about 1% and R went down a bit. I am wondering what happened here. Also Rfree always went down after TLS refinement but always went up a lot more after the individual ADP refinement. Is there anything I can do here? Should I use weaker B restraints? I tried to assign a wxu_scale value. But phenix.refine automatically adjust it to 1.81 every time. ------------------------------------------------------------------------ R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3982 0.5701 6.156859e+00 6.238509e+00 1_bss: 0.2008 0.2494 5.949117e+00 6.088855e+00 1_xyz: 0.2030 0.2497 5.953829e+00 6.091696e+00 1_adp: 0.1998 0.2559 5.952833e+00 6.099340e+00 2_bss: 0.1996 0.2557 5.952517e+00 6.099196e+00 2_xyz: 0.1984 0.2576 5.953246e+00 6.104085e+00 2_adp: 0.1974 0.2578 5.950434e+00 6.102336e+00 3_bss: 0.1972 0.2574 5.950333e+00 6.102222e+00 3_xyz: 0.1997 0.2576 5.956524e+00 6.103647e+00 3_adp: 0.1987 0.2590 5.955554e+00 6.104434e+00 3_bss: 0.1986 0.2588 5.955445e+00 6.104227e+00 ------------------------------------------------------------------------ Weights for target T = Exray * wxc * wxc_scale + Echem * wc and angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites) stage wxc wxu wxc_sc wxu_sc /_gxc,gc /_gxu,gu 0 : 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_bss: 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_xyz: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 1_adp: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_bss: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_xyz: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 2_adp: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_bss: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_xyz: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_adp: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_bss: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 ------------------------------------------------------------------------ Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

3 9

Postdoctoral Position for PHENIX development
by Paul D. Adams 03 Aug '07

03 Aug '07

======================================================================= Lawrence Berkeley National Laboratory Computational Postdoctoral Fellow ======================================================================= Computational Postdoctoral Fellow Job ID: 20907 Division: Physical Biosciences Date Opened: 8/2/2007 Summary We are seeking an intelligent, motivated scientist to develop graphical tools for the PHENIX software system. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities will include development and implementation of graphical interfaces, user workflow tools, and mechanisms for data tracking and storage. Duties Essential - Primary duties and responsibilities will include development and implementation of computational algorithms for structure determination using X-ray crystallography. Develop graphic interfaces to components of the PHENIX software system. Create interfaces between PHENIX and other software packages such as Coot. Implement software code for capturing and tracking data and other information as it is created by the PHENIX software. This position requires interaction with P.I.s, postdocs, Scientists and external collaborators involved in the PHENIX project. Publication of research results in scientific journals and presentation of results at scientific meetings. Marginal - Actively participate in group meetings. Assume shared responsibility for maintenance of computational equipment with other group members. Qualifications Essential - Ph.D. within the last three years in computational crystallography or a related field. Demonstrated experience with graphical interface development. First-author publications in macromolecular crystallography or closely related field. Familiarity with software development tools such as C++, C or Fortran programming languages and scripting languages such as Python or Perl. Strong programming skills. Solid interpersonal skills and the ability to work in a team environment are critical. Marginal - Experience with the practical aspects of protein crystallography: protein production, crystallization and structure solution. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about PHENIX visit: http://www.phenix-online.org/ For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20907. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

1 0

estimated coordinate error
by Jianghai Zhu 02 Aug '07

02 Aug '07

Hi, I am refining a 2.6 A structure using both phenix.refine and refmac5. Both programs give me similar R and Rfree values. But the estimated coordinate errors are quite different. From phenix.refine: maximum likelihood estimate for coordinate error: 0.42 A From refmac5: estimated overall coordinate error: ESU based on R value: 0.427 A ESU based on Free R value: 0.293 A ESU based on maximum likelihood: 0.239 A I am wondering why they are different. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

3 4

General Question !!!
by john kryst 02 Aug '07

02 Aug '07

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

5 6

AutoSol problem
by Ben Eisenbraun 01 Aug '07

01 Aug '07

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

2 2

TEST - please ignore
by Luca Jovine 31 Jul '07

31 Jul '07

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

1 0

A question about AutoBuild
by Marcelo Carlos Sousa 31 Jul '07

31 Jul '07

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

2 1

part II. A question about autobuild
by Marcelo Carlos Sousa 31 Jul '07

31 Jul '07

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

1 0

R-factor problem !!!
by john kryst 31 Jul '07

31 Jul '07

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

5 7

problems with clashes
by Lari Lehtio 31 Jul '07

31 Jul '07

Hi, I nowadays use phenix.refine almost always in the first stages of the refinement and later usually move to refmac. Now I have two modest resolution structures which behave much better in phenix than in refmac. In addition to the more tedious deposition (I guess), I have a problem with clashes. When I analyse the structures with molprobity, I get much better clashscores with refmac refined files. Is there a way to increase the restraint for these contacts or should I just keep decreasing the wxc_scale (from the default)? Rmsds reported by refmac (0 cycles) for bonds and angles are already lower than what I'm used to. B-factors on the other hand seem to be less restrained in phenix. ~Lari~ _______________________________________ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________

5 8

Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 28 Jul '07

28 Jul '07

Hi Jianghai, > I tried "discard_psi_phi=False" in phenix.refine. There is only > slightly improvement in the R, Rfree, and ramachandran plot (about > 0.2% less disallowed residues, wxc_scale=0.2). A structure > optimization (wxc_scale=0) with the phi-psi restraints has a bigger > impact (about 2% less disallowed residues) with about 2% higher > Rfree. Thanks for your feedback! > What do you think is a good value for wxc_scale in a low-resolution > refinement? This is a tough one to answer. wxc_scale reflects how much you trust your data to guide you to the best model. That depends on many influences. I think the best - although expensive - approach is to simply try a range of values. Note that the esd on the psi-phi restraints are just someone's (?) best guesses. It may be worth playing with these values as well. For that, copy the data_link_TRANS, data_link_PTRANS, data_link_CIS, and data_link_PCIS blocks from mon_lib_list.cif to a new files, change the values, then specify the file on the phenix.refine command line. (You may want to double-check in the .geo file that your new values are actually used.) > What is the difference between wxc_scale=0 and > phenix.geometry_minimization? Should basically be the same, but in phenix.refine you can override parameters like discard_psi_phi. phenix.geometry_minimization doesn't allow you to do this (it is one of those many little things I never got to). Ralf

1 0

Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 26 Jul '07

26 Jul '07

Hi Jianghai, > I am refining a low resolution huge protein structure. There are > about 20% residues in the disallowed region of ramachandran plot. Is > there a way in phenix.refine to refine the phi, psi angles to get a > better ramachandran plot? or a phi, psi restraints in refinement? If you add discard_psi_phi=False to the phenix.refine command line the psi and phi dihedral angles are restraint according to the CCP4 monomer library definitions in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get the full path name). Look for data_link_TRANS and data_link_CIS, scroll down to _chem_link_tor.value_angle, to see the restraint definitions. We don't have much experience using the phi, psi restraints. If you don't mind, please let us know how it goes! Ralf

4 5

ramachanran plot refinement or restraint?
by Jianghai Zhu 26 Jul '07

26 Jul '07

Hi, I am refining a low resolution huge protein structure. There are about 20% residues in the disallowed region of ramachandran plot. Is there a way in phenix.refine to refine the phi, psi angles to get a better ramachandran plot? or a phi, psi restraints in refinement? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

2 1

problems in installation of phenix
by tara kashav 26 Jul '07

26 Jul '07

Dear all, I am trying to install phenix but getting following error. My system specifications are: 2.6.5-1.358 i686. Can anyone suggest me how to troubleshoot and install the program. Traceback (most recent call last): File "/usr/local/phenix-1.3b/phenix/wxGUI/wxPhenix.py", line 11, in <module> import wx File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libXfixes.so.3: cannot open shared object file: No such file or directory Thanks, Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

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Re: [phenixbb] How to keep a custom bond planar ?
by Ralf W. Grosse-Kunstleve 25 Jul '07

25 Jul '07

Hi Mathieu, Also sorry for the late reply. > How can I define a plan or some dihedral ?? Sorry, this is not implemented (not hard, but never got to it). > Or as in the ligand .cif I defined a plan > LIG plan-2 C1 0.020 > LIG plan-2 C2 0.020 > LIG plan-2 C3 0.020 > > I could add the atoms NZ and CE of the lysine to the plan-2. You can define the bond, angles, dihedrals, chiralities and planarities with a cif link. Currently we don't generate such links automatically (it is in the works). To get a start, copy one of the links from the mon_lib_list.cif file; the command phenix.where_mon_lib_list_cif will give you the absolute path. Give the cif link a unique name and modify it for your situation. Then use "apply_cif_link" as described in the phenix.refine documentation, e.g. at the CCI Apps download page (http://www.phenix-online.org/download/cci_apps/). Let me know if you need more specific help. Ralf

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Re: [phenixbb] handling of alternate conformations
by Ralf W. Grosse-Kunstleve 25 Jul '07

25 Jul '07

Hi Ulrich, Sorry for the late reply. I was out of town for a week. > My first question is whether NCS constraints are also applied to alternate > conformations. Should be, but is not heavily tested. All NCS restraints are listed in the .geo file created by phenix.refine (assuming write_geo_file=True, which is the default). Look for the long lists following "NCS restraint group". Do your alternative conformation atoms appear in these lists? > My second question concerns the atom count of the conformers, where the > parts with non-alternating conformations seem to be included as well. Pavel's explanation from last week is correct. Internally a "conformer" is always a complete chain. The bond, angle, dihedral, chirality, and planarity restraints are determined independently for each conformer. This generates duplicate restraints which are checked for consistency and then reduced again. Ralf

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handling of alternate conformations
by Ulrich Baumann 17 Jul '07

17 Jul '07

Dear Phenix experts, we encounter the following "problem" when trying to refine alternating conformations: we have a complex with 4 chemically different polypeptide chains in the asymmetric unit, composition A3B3CD. For chains C and D we see additional density, which appears to belong to three alternating conformations which can be thought as rigid-body motions (for the whole chains C and D, let's call these conformers 1,2 and 3, but we label them conventionally in the file with the prefix A,B,and C) with roughly estimated occupancies of about 0.3, 0.3 and 0.4 (we can really see most of them). A and B have no visible alternating conformations (occupancies set to 1.0). From the atom count it appears that phenix reads in three conformers called A,B and C with A: A3B3C(1)D(1), B: A3B3C(2)D(2) and C: A3B3C(3)D(3). Phenix.refine says it has these 3 conformers: conformer A A:2700 atoms, conformer B:2700 atoms, common with A 2100, conformer C:2700 atoms, common with A 2100, common with B 2100. Refinement yields an R/Rfree of about 0.210/0.325. If we treat the three conformers of polypeptide chains C and D as independent chains with occupancy each 1.0 (this is possible 'cos there are no repulsive contacts between them, fortunately), we get R/Rfree of 0.243/0.291 and phenix applies NCS restraints to all chains. The resolution is about 2.9 A. We use phenix.refine from the CCI_APPS, version 2007-03-26-1903, SUSE Linux. My questions is: is the difference due to the lack of NCS between conformers or are the occupancies mistreated somwhow? I am asking because I would not consider the whole A3B3C(x)D(x) particle as a conformer but only chains C and D ...... Is there a possibility to apply NCS restraints to conformers? Many thanks in advance, Ulrich

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How to keep a custom bond planar ?
by Coincon Mathieu 17 Jul '07

17 Jul '07

Hi, I defined a bond (and angles) between my ligand and the NZ of a lysine in a file (bond.def). ..-C2-.. | -CE-NZ = C1-C3-.... This is a double bond. Everything work good except for the planarity of the lysine's atoms. For the bond I wrote in my bond.def: bond { action = *add atom_selection_1 = chain D and resname LIG and name C2 atom_selection_2 = chain A and resname LYS and resid 66 and name NZ distance_ideal = 1.340 sigma = 0.02 } For an angle: angle { action = *add atom_selection_1 = chain D and resname LIG and name C3 atom_selection_2 = chain D and resname LIG and name C2 atom_selection_3 = chain A and resname LYS and resid 66 and name NZ angle_ideal = 120.000 sigma = 3 } How can I define a plan or some dihedral ?? Or as in the ligand .cif I defined a plan LIG plan-2 C1 0.020 LIG plan-2 C2 0.020 LIG plan-2 C3 0.020 I could add the atoms NZ and CE of the lysine to the plan-2. Thanks by advance. And by the way phenix (with coot) is GREAT (I did my apo-enzyme in four days !!!!) -------- Mathieu Coicon PhD Student Biochimie Universite de Montreal (+1)514-343-6111 #5352

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Phaser
by john kryst 13 Jul '07

13 Jul '07

Hi all !!! Is it possible to fix one domain and search for the second one in phaser !!! What are the keywords to use for that. I have a protein with two domains. It i give both the domains together it is not finding the solution. If i give only one domain it is giving the solution and the R and Rfee is 28 and 33. But it is not finding the second one. Thanks in advance for your suggestions.. regards John

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Refinement use of Friedel pairs
by Mark A Saper 12 Jul '07

12 Jul '07

I am refining a structure containing SeMet with data collected at peak wavelength. Provided I give the f' and f'', will phenix.refine calculate F+ and F- structure factors and use the provided FOBS+ and FOBS- ? CNS does this. Refmac only uses f' and I get >6 sigma Fo-Fc peaks on the Se. Thanks for your help. _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

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setting resolution for 2 datasets in AutoSol
by Thomas C. Terwilliger 10 Jul '07

10 Jul '07

Hi Luca, It's easiest to do this in 2 steps: 1a. You can set the resolution separately for each dataset in the AutoSol Wizard. In the GUI, just go through each dataset and set the overall resolution to your desired values as you go. Ignore the density modification and building that occurs in this run. 1b. Then you'll get an output exptl_fobs_phases_freeR_flags_2.mtz or equivalent that is phased to the resolution you specified, but that has all the data (with no phases) to higher resolution. 2. Now run the AutoBuild wizard, and set the resolution to your high-resolution limit. That should use the phases you generated, and include the high-res data for density modification and refinement. Equivalently, you can run AutoSol at low resolution then run AutoBuild at higher resolution by supplying an input_hires_file with the hires data. A key point here is that the building in AutoSol is just a preliminary build...the building in AutoBuild is the real thing. You can also run 2 datasets and set the resolution for each in a script. Here is a script to read in 2 SAD datasets and solve them together as one, setting the resolution of phasing to 3 A for the first and 2.9 for the second, cat two_datasets.inp input_seq_file seq.dat resolution 2.9 # Resolution expt_type sad input_file_list se.sca ############## NEW DATASET ################ run_list start # run "start" method. run_list read_another_dataset # starting a new dataset here resolution 3.1 # Resolution input_file_list br.sca Let me know if that does not do it! -Tom T >> From: lp212(a)mole.bio.cam.ac.uk >> Date: July 9, 2007 3:38:28 PM PDT >> To: phenixbb(a)phenix-online.org >> Subject: script for Zn and Se phasing >> Hi, >> I have collected two peak datasets on two different crystals, for a protein that contains zinc: >> 1. peak dataset at the Zn edge (lambda=1.285A, 2.5A reso) >> 2. peak dataset at the Se edge (lambda=0.98A, 2.8A reso) >> The protein has 2 Zn and 11 SeMet, and 4/au. When I input both >> datasets in the AutoSol GUI, Hyss finds correctly 8/8 Zn sites, and ~34/44 Se sites, but only when I cut back the resolution (4.2A for Zn, and 4.7A for Se). What I can't figure out is how to tell the Autosol GUI to use a low-res cutoff for finding the sites, and then use all the data for model building. Could someone please explain how to do this in the GUI, or send me a script? >> Thanks a lot! Apologies if this is trivial... >> Luca >

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Re: [phenixbb] depositing phenix-refined coordinates
by Ralf W. Grosse-Kunstleve 06 Jul '07

06 Jul '07

Hi Enrico, > However, I would be very grateful if someone could point me to the topic > already posted in the message below by Dr. Scott few days ago, > exactly at: > "a quick description for depositing phenix-refined coordinates?", > though the full message contained very interesting points I would > love to hear about We don't have a dedicated deposition tool yet, sorry. But we are actively working with the PDB on this. In the meantime, the .pdb files produced by phenix.refine are the best starting point. > (I also performed refinement by refmac/phenix, and observed kind of a > similar trend for those numbers). It may be because we are reporting mean deviations instead of root-mean-square deviations. This is kind of an oversight on our part and will be changed in the next version. Ralf

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CCI-Apps Verisons vs. Phenix Versions
by Schubert, Carsten [PRDUS] 06 Jul '07

06 Jul '07

Hi, Quick question about versions of CCI-Apps as standalones and in phenix. How does once decide which version of the CCI-Apps is more current? I have not looked in depth, but is there a equivalent build tag for the CCI-Apps in phenix as the one for the CCI-Apps. Currently I am assuming that the CCI-Apps are alway more up to date, but that may not hold true for the upcoming phenix 1.3 release. Thanks Carsten

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some general refine questions
by William Scott 05 Jul '07

05 Jul '07

Hi folks: With the helpful advice of the phenix crew, I've re-refined 2goz, an entry in the pdb in which I used refmac5 the first time around. There was a small error in the pdb: One nucleotide (C8 in chain A) was rotated 180 degrees about the glycosylic bond from where it should have been. The net result is one oxygen atom was in the wrong place in the structure, and this was apparent within the difference Fourier. After I rotated the base and re-refined in refmac, the Rfactor and other stats remained essentially unchanged (so this fix has nothing to do with the following): My refinement results in Refmac: REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.241 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1503 ; 0.009 ; 0.021 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2331 ; 1.676 ; 3.000 Then I refined in phenix. I get REMARK Final: r_work = 0.1737 r_free = 0.2224 bonds = 0.003 angles = 0.745 So the working and free R factor are both lower, and the geometry is substantially tighter. If I relax the weights in phenix, even to get rms bonds of around 0.006, the free-R goes up, which tells me this is not something I am justified in doing. Phil Evans once told me that anything tighter than about 0.01 (conservatively) was science-fiction, in that this is within the error of the idealized libraries for bond lengths. Other people have asked me about this too, and I didn't know how to reply. Is bonds = 0.003 angles = 0.745 realistic, or have I done something wrong? Even if I do structure idealization in Refmac, I can't get the rms bonds below about 0.005 (and my understanding is that it uses the same monomer library). Why is the weight multiplied by 0.5 by default? Since changing that to 1.0 slightly increases freeR, I assume it is the default for some reason. All the best, Bill PS: Could someone point me to a quick description for depositing phenix-refined coordinates? (The latest phenix installer seems to have omitted the docs.) William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott

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Re: [phenixbb] sugar links in phenix.refine
by Ralf W. Grosse-Kunstleve 05 Jul '07

05 Jul '07

Almost, but you need a separate scope (thing between braces) for each link, e.g.: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } refinement.pdb_interpretation.apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } Or alternatively: refinement.pdb_interpretation { apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } } Ralf

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Re: [phenixbb] Multivariate Z score L-test
by Claudia Scotti 29 Jun '07

29 Jun '07

Thank you so much. I'll try all the space groups and see what happens. Many thanks again, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ---------------------------------------- > Date: Fri, 29 Jun 2007 07:35:22 -0700 > From: PHZwart(a)lbl.gov > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Multivariate Z score L-test > > Hi Claudia, > > This could indicate that tyour data is actually P 2 1 1, P 1 2 1 or P > 1 1 2 or P 21 1 1, P 1 21 1, P 1 1 21. Try processing that data in > those spacegroups and see if that makes any difference. You might end > up havig to refine your structure in all spacegroups to find out which > possibility is the best. > > It could also indicate that the quality of your data is not very good, > either due to suboptimal data processing or because of bad diffraction > (or both). > > HTH > > Peter > > > 2007/6/29, Claudia Scotti : > > > > Dear List, > > > > I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44. > > > > I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. > > Matthews coefficient suggests two molecules per asu. > > No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. > > MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent. > > > > When refining, refinement gets stuck as I mentioned above. > > > > I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data. > > > > Sorry for the probably trivial question and for probably missing important data. > > > > Thanks a lot for any help and suggestions, > > > > Claudia > > > > ------------------------------------------------------------------------------- > > Twinning and intensity statistics summary (acentric data): > > > > Statistics independent of twin laws > > - /^2 : 1.827 > > - ^2/ : 0.838 > > - : 0.649 > > - , : 0.417, 0.242 > > Multivariate Z score L-test: 6.305 > > The multivariate Z score is a quality measure of the given > > spread in intensities. Good to reasonable data is expected > > to have a Z score lower than 3.5. > > Large values can indicate twinning, but small values do not > > neccesarily exclude it. > > > > > > No (pseudo)merohedral twin laws were found. > > > > > > Patterson analyses > > - Largest peak height : 11.094 > > (correpsonding p value : 1.080e-01) > > > > > > The largest off-origin peak in the Patterson function is 11.09% of the > > height of the origin peak. No significant pseudotranslation is detected. > > > > The results of the L-test indicate that the intensity statistics > > are significantly different then is expected from good to reasonable, > > untwinned data. > > As there are no twin laws possible given the crystal symmetry, there could be > > a number of reasons for the departure of the intensity statistics from normality. > > Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems > > as well as bad data quality might be possible reasons. > > It could be worthwhile considering reprocessing the data. > > ----------------------------------------------------------------------------------------------- > > > > Claudia Scotti > > Dipartimento di Medicina Sperimentale > > Sezione di Patologia Generale > > Universita' di Pavia > > Piazza Botta, 10 > > 27100 Pavia > > Italia > > Tel. 0039 0382 986335/8/1 > > Facs 0039 0382 303673 > > > > _________________________________________________________________ > > Express yourself instantly with MSN Messenger! Download today it's FREE! > > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > _______________________________________________ > > 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 _________________________________________________________________ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TX…

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Multivariate Z score L-test
by Claudia Scotti 29 Jun '07

29 Jun '07

Dear List, I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44. I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. Matthews coefficient suggests two molecules per asu. No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent. When refining, refinement gets stuck as I mentioned above. I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data. Sorry for the probably trivial question and for probably missing important data. Thanks a lot for any help and suggestions, Claudia ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - /^2 : 1.827 - ^2/ : 0.838 - : 0.649 - , : 0.417, 0.242 Multivariate Z score L-test: 6.305 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 11.094 (correpsonding p value : 1.080e-01) The largest off-origin peak in the Patterson function is 11.09% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are no twin laws possible given the crystal symmetry, there could be a number of reasons for the departure of the intensity statistics from normality. Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems as well as bad data quality might be possible reasons. It could be worthwhile considering reprocessing the data. ----------------------------------------------------------------------------------------------- Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

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sugar links in phenix.refine
by Jianghai Zhu 22 Jun '07

22 Jun '07

Hi, How does phenix.refine handle the sugar links in refinement? I suppose phenix.refine will automatically recognize NAG and MAN. Will it recognized NAS-ASN, beta1-4, alpha1-4, etc linkages between sugars? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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'Tasks' tab missing from 1.3b GUI and HL coefficients from a model
by Stephen Graham 22 Jun '07

22 Jun '07

Hi all, I recently (well, yesterday) installed the latest beta of phenix and everything is working great from the command line (which is how I use phenix 99.9% of the time). However, I fired up the GUI and found that the 'Tasks' tab appears to be missing from the 'Strategy Interface'. Is this a bug, a manifestation of an installation problem, or a feature? And... I was trying to use the GUI for prime-and-switch phasing to improve the maps for a partly-refined MR solution. What is the recommended path for creating HL coefficients from a model (from simulated annealing in phenix.refine) so that I can use the GUI's resolve 'prime-and-switch' strategy? Or is there an even better way of removing model bias and density-improving a big, low-res, MR-solved structure with 4-fold NCS in phenix? Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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harmonic restrains in phenix.refine
by Bjørn Pañella Pedersen 22 Jun '07

22 Jun '07

Hi all, Is it possible to use harmonic restrains in phenix.refine, in a manner similar to CNS v1.2? I have searched the phenix.refine documentation and the web, but can't find anything. I use version 2007_04_06_1210 of phenix. Thanks! -Bjørn -- Bjørn Pañella Pedersen Ph.D Student, MSc Department of Molecular Biology Office: +45 89425021 University of Aarhus Lab: +45 89425010 Gustav Wieds Vej 10c Email: bpp(a)mb.au.dk DK-8000 Aarhus C Lab WWW: http://www.bioxray.dk Denmark

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SAD + MR
by Lucas Bleicher 20 Jun '07

20 Jun '07

I have a dataset from a Cs-soaked crystal, and the protein has a domain solved in the PDB. The problem is that the map obtained just with the experimental phasing is not so easily interpreted, and the domain is just about 25% of the whole protein. Inspection of the map generated by MR suggests that it's a good solution, with residues fitting reasonably well on the density. Given the new features on Phaser 2.0, which I suppose is included in Phenix 1.3b, can anyone suggest a protocol to profit from both things (anomalous scattering + good search model)? Thanks in advance, Lucas ____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso

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Death by Big-ass structure&[email protected]
by Kate Kavanagh 14 Jun '07

14 Jun '07

Hi Peter, The reindexing works fine but when I try to convert back to R3:H all atoms with ANISOU records are given B-factors of -79.86: ATOM 1 N MET A 1 16.402 60.069 44.768 1.00-78.96 N ATOM 2 CA MET A 1 16.316 58.621 44.978 1.00-78.96 C ATOM 3 CB MET A 1 17.622 57.922 44.573 1.00-78.96 C ATOM 4 C MET A 1 15.966 58.300 46.432 1.00-78.96 C ATOM 5 O MET A 1 16.196 59.115 47.326 1.00-78.96 O ATOM 6 N PHE A 2 15.408 57.114 46.661 1.00-78.96 N ATOM 7 CA PHE A 2 15.047 56.686 48.013 1.00-78.96 C ATOM 8 CB PHE A 2 13.750 55.866 48.016 1.00-78.96 C ATOM 9 CG PHE A 2 13.323 55.436 49.391 1.00-78.96 C ..... And since TLS refinement has been used, all protein atoms have ANISOU records. Any suggestions? Kate

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Re: [phenixbb] [ccp4bb] DANO from PDB
by Peter Zwart 08 Jun '07

08 Jun '07

Hi Santosh, Here is an alternative to methods mentioned earlier. If you get the latest version of the cctbx or cci_apps (from www.phenix-online.org) you will find a new application named phenix.xmanip (or mmtbx.xmanip if you only download the cctbx). xmanip has some useful features, one of them is that one can provide pieces of python code to the interface that will be executed. You have full access to all cctbx methods available. Please find below an example parameter file that perform structure factor calculation (in less than 90 lines of code and input) that includes elements with f" and f' not being equal to zero (you have to set the values of f" and f' yourself rather then rely on lookup tables by wavelength) and allows you to set bulk solvent parameters such as ksol, bsol and the overall anisotropic B of the data (B_cart). Save the text below (between the hash-es in a file named params.def , change the unit cell and sg parameters, the input pdb file and f" and f' value dictionary to suit your needs: ( like fp_dict = { "S": 0, "C": 0 } fdp_dict = { "S": 0, "C": 2.8 } for instance } You can fool around with solvent density, solvent B, overall scale factor and overall anisotropic B value and resolution (d_min). Then run phenix.xmanip params.def and get a file named xmanip.mtz that will contain your error free data. If you want, you can add uniform or Gaussian errors yourself. Since xmanip is fairly new, you will find a bug in the current release that somehow appears when you do not read in any external xray data. This happens however right after the mtz file in question has been written out. This will be fixed in the forthcoming release (soonish). Let me know if anything is unclear or if you have trouble running it. HTH Peter Zwart ################################################################### xmanip { input { unit_cell = "80.127 80.127 71.582 90.00 90.00 120.00" space_group = R3:H model { file_name = tst.pdb } } parameters { action = reindex manipulate_pdb *manipulate_miller manipulate_miller { task = get_dano get_diso lsq_scale sfcalc *custom None output_label_root = "Imock" custom{ code = """ #------------------------------------------------------- # This you can change if desired # # Dictionary for fp and fpp values fp_dict = { "Zn": -0.189 } fdp_dict = { "Zn": 4.898 } # final resolution of the data d_min = 2.0 # anisotropic B value b_cart = [ 0, 0, 0, 0, 0, 0 ] # solvent parameters k_sol = 0.35 b_sol = 45.0 # overall scale k_overall = 1.0 #------------------------------------------------------- # below this point, things should be more or less okai # from mmtbx import f_model from cctbx.xray import observation_types #loop over all scatterers in the xray structure #print >> out, dir(xray_structure) scatterers = xray_structure.scatterers() for atom in scatterers.as_1d(): if fp_dict.has_key( atom.element_symbol() ): atom.fp = fp_dict[ atom.element_symbol() ] if fdp_dict.has_key( atom.element_symbol() ): atom.fdp = fdp_dict[ atom.element_symbol() ] #the changes have been made to fp and fdp #Now we have to do some trickery to get some fobs with bulk solvent #contribution ... #First make a 'fake' set of f_obs fake_f_obs = abs(xray_structure.structure_factors( d_min = d_min, anomalous_flag = True ).f_calc()) # make a 'fake' set of free flags fake_free_flags = fake_f_obs.generate_r_free_flags(fraction = 0.1, max_free = 99999999) fmodel = f_model.manager( xray_structure = xray_structure, r_free_flags = fake_free_flags, target_name = "ls_wunit_k1", f_obs = fake_f_obs, b_cart = b_cart, k_sol = k_sol, b_sol = b_sol, overall_scale = k_overall ) # now get the final values of F+ and F-. # Note the abs to get amplitudes only result = abs( fmodel.f_model() ).set_observation_type( observation_types.amplitude() ) # you want make this into intensities? result = result.f_as_f_sq() # lets leave the intensities alone for now, and just make 'mock' sigmas # to statisfy certain programs. # Don't forget to set the observation type! sigmas = result.data()/100.0 result = result.customized_copy(data = result.data(), sigmas=sigmas).set_observation_type(result) #By default, a parameter named result is passed back to the xmanip #routines and will be written to the final mtz file """ } } } output { logfile = "xmanip.log" hklout = "xmanip.mtz" xyzout = "xmanip.pdb" } } ################################################################### Santosh Panjikar wrote: > Hi all, > > Does anybody have a program which can calculate anomalous differences or > F+ and F- from a refined structure at given wavelength and resolution ? > > Thanks > Santosh > > > Santosh Panjikar, Ph.D. panjikar(a)embl-hamburg.de > Staff Scientist > EMBL Hamburg outstation http://www.embl-hamburg.de/~panjikar/ > DESY, Notkestrasse 85 Tel.:+49-40-89902-141 > 22603, Hamburg, Germany Fax: +49-40-89902-149

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removing Van der Waals repulsion between two atoms
by Miguel Ortiz-Lombardía 07 Jun '07

07 Jun '07

Dear all, I've a question regarding phenix.refine. Is it possible in phenix.refine to remove repulsion between a couple of atoms to see to what distance they refine when unrestrained? I'm thinking in something like what in CNS/XPLOR one would do by setting: igroup interaction (selection1) (selection2) weights * 1 vdw 0. elec 0. end end I've been searching the web for a solution to this question, but haven't come up with anything. Sorry if I missed it! I would appreciate your help. Cheers, Miguel -- correo-e: ibdeno(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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Re: [phenixbb] how to add phase info to the autosol wizard
by Thomas C. Terwilliger 06 Jun '07

06 Jun '07

Hi again Chuanbing, I'm sorry, I mean 1.3b-d5 (d4 is just about to be released). -Tom T Hi Chuanbing, It will be available in version 1.3b-d4 which has yet to be released (or even built)...it takes a little time between the time I have put the code in and the time that it gets to you, unfortunately! -Tom T > Dear Tom, > > Thank you very much! It's expected! > I am using the Version 1.24.1b, is version 1.3 the next version you > mentioned? > > Chuanbing > > > > On 6/5/07, Tom Terwilliger <terwilliger(a)lanl.gov> wrote: >> >> Hi Chuanbing, >> >> I have added this to the AutoSol wizard >> (input_phase_file=my-phases.mtz) and the next version of PHENIX will have >> it. >> >> -Tom T >> >> At 01:51 AM 5/31/2007, CB Bian wrote: >> >Dear all, >> > >> > I am trying to add phase info from externally calculated >> > phases to the autosol wizard with S-SAD data. But I can not find the option to do it in the running. Can someone help me? >> > >> > >> >Thanks in advance >> > >> >Chuanbing >> > >> >-- >> >ChuanBing Bian, Ph.D Student >> >Structural biology group >> >State Key laboratory of Structural Chemistry >> >Fujian Institute of Research on the Structure of Matter, >> >Chinese Academy of Sciences >> >155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China >> >E-mail: >> ><mailto:[email protected]>cbbian(a)gmail.com >> ><mailto:[email protected]> cbbian(a)fjirsm.ac.cn >> >Tel:(office)+86-591-8370-5814 >> ><http://protein.fjirsm.ac.cn/>http://protein.fjirsm.ac.cn >> >_______________________________________________ >> >phenixbb mailing list >> >phenixbb(a)phenix-online.org >> >http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: >> http://www.doe-mbi.ucla.edu/TB >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: >> http://www.doe-mbi.ucla.edu/TB >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > > -- > ChuanBing Bian, Ph.D Student > Structural biology group > State Key laboratory of Structural Chemistry > Fujian Institute of Research on the Structure of Matter, > Chinese Academy of Sciences > 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China > E-mail: cbbian(a)gmail.com cbbian(a)fjirsm.ac.cn > Tel:(office)+86-591-8370-5814 > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] how to add phase info to the autosol wizard
by Tom Terwilliger 06 Jun '07

06 Jun '07

Hi Chuanbing, I have added this to the AutoSol wizard (input_phase_file=my-phases.mtz) and the next version of PHENIX will have it. -Tom T At 01:51 AM 5/31/2007, CB Bian wrote: >Dear all, > > I am trying to add phase info from externally calculated > phases to the autosol wizard with S-SAD data. But I can not find > the option to do it in the running. Can someone help me? > > >Thanks in advance > >Chuanbing > >-- >ChuanBing Bian, Ph.D Student >Structural biology group >State Key laboratory of Structural Chemistry >Fujian Institute of Research on the Structure of Matter, >Chinese Academy of Sciences >155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China >E-mail: ><mailto:[email protected]>cbbian(a)gmail.com ><mailto:[email protected]>cbbian(a)fjirsm.ac.cn >Tel:(office)+86-591-8370-5814 ><http://protein.fjirsm.ac.cn/>http://protein.fjirsm.ac.cn >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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secondary structure restraint
by Jianghai Zhu 06 Jun '07

06 Jun '07

Hi all, I am refining a low resolution structure (~3.8 A). For some of the domains in the structure, we already have high resolution structures. Despite of some conformational changes in some loops, the core structures should be the same. I am wondering if it is possible to restrain the secondary structures in phenix.refine. Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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phenix.refine crashed
by Jianghai Zhu 06 Jun '07

06 Jun '07

Hi, In my refinement phenix.refine crashed with the following errors. ================================ xyz refinement =============================== Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1310, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 733, in refinement_machine h_params = h_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 136, in __init__ ignore_line_search_failed_step_at_lower_bound = True)) File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 242, in run log) File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 121, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 369, in compute_functional_and_gradients u_iso_refinable_params = u_iso_refinable_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 224, in compute_target sf_v3d_sel = sf_v3d.set_selected(self.hd_selection, [0,0,0]) RuntimeError: scitbx Internal Error: /net/sharptail/scratch1/rwgk/ auto_build/sources/scitbx/include/scitbx/array_family/boost_python/ flex_wrapper.h(473): SCITBX_ASSERT(a.accessor() == flags.accessor()) failure. What happened here? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Re: [phenixbb] elbow.builder
by William Scott 05 Jun '07

05 Jun '07

Problem solved: The OS X pre-compiled distribution comes with an executable gamess.Mar242007R1.x but the shell script seems to require gamess.00.x so in /usr/local/gamess I did this: sudo ln -s gamess.Mar242007R1.x gamess.00.x and benzene is as one would expect. BTW, when I run this under tcsh, I get a more informative error message -- it says it can't find gamess. Under zsh, it just says "Failed to read coordinates. Aborting optimisation." Anyway, it all works now. Thanks. Bill On Jun 3, 2007, at 3:08 PM, Peter Zwart wrote: > gamess is installed right? > > P > > > > 2007/6/3, William Scott <wgscott(a)chemistry.ucsc.edu>: >> actually, "small distortions" was too optimistic: >> >> http://chemistry.ucsc.edu/~wgscott/temp/benzene.png >> >> >> >> >> On Jun 3, 2007, at 2:33 PM, William Scott wrote: >> >> > Hi folks: >> > >> > I've been playing around a bit with elbow.builder, and found the >> > following: >> > >> > -------------- >> > >> > >> > elbow.builder --opt --smiles c1ccccc1 >> > >> > gives me a nice, flat, hexagonal benzene >> > >> > elbow.builder --gamess --smiles c1ccccc1 >> > >> > gives me a benzene that is slightly bent out of plane and has other >> > small distortions with respect to 6-fold symmetry. >> > >> > Is this a problem with elbow, a problem with gamess, or a Jahn- >> > Teller effect? >> > >> > >> > ------------ >> > >> > >> > >> > Also, I noticed elbow.doc requires a mozilla or netscape >> > executable. Since both of these are obsolete, maybe a firefox >> > executable should be an option? On OS X, "open" should open a URL >> > in the user's favorite browser, but it doesn't seem to work right >> > with Safari (which stupidly opens a Finder window of the directory >> > containing the html file). My workaround was to make a shell >> > script called "mozilla" that invokes Camino: >> > >> > #!/bin/zsh -f >> > /usr/bin/open -a Camino "$@" >> > >> > HTH someone. >> > >> > ------------------ >> > >> > >> > Bill >> > >> > >> > >> > >> > William G. Scott >> > >> > contact info: http://chemistry.ucsc.edu/~wgscott >> > >> > >> > >> > >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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