ó ±™xTc@ sjddlmZddlZddlmZddlZddlZddlZddl Z ddl m Z ddl mZddlZddl mZddl mZddl mZdd lmZejd ƒejd ƒd Zd Zd „Zejeed„Zdejfd„ƒYZdd„Z!d„Z"d„Z#e$dkrfedej%dƒndS(iÿÿÿÿ(tdivisionN(tflex(tSorry(t runtime_utils(treflection_file_reader(treflection_file_utils(tcrystal_symmetry_from_any(tcrystalis phenix.maps: a command line tool to compute various maps and save them in most of known formats. How to run the command line version: 1. Run phenix.maps without any arguments: just type phenix.maps in the command line and hit Enter. This will creare a parameter file called maps.params, which can be renamed if desired. 2. Edit maps.params file to specify input/output file names, data labels and the desired maps. It is possible to request as many maps as desired. By default, the file maps.params specifies 5 maps to be created: 2mFo-DFc, 2mFo-DFc with missing Fobs filled with DFcalc, mFo-DFc and anomalous difference maps will be output in MTZ format, and one 2mFo-DFc map will be output in CCP4 format. NOTE: the anomalous difference map will only be created if the input reflection data file contains Bijvoet maps (F+/F- or I+/I-). 3. Run this command to compute requested maps: phenix.maps maps.params Alternately, you may specify input files (and additional parameters) directly on the command line: % phenix.maps model.pdb data.mtz and it will automatically generate the default maps as described above. Important Facts: - phenix.maps is available in PHENIX GUI. - The scope of parameters 'map_coefficients' defines the map that will be output as Fourier map coefficients. The scope of parameters 'map' defines the maps that will be output as CCP4 or X-plor format. - To create several maps: duplicate either 'map_coefficients' or 'map' or both scopes of parameters as many times as many maps is desired. Then edit each of them to define the maps. - A map is defined by specifying a map type using 'map_type' keyword available within each scope of parameters: 'map_coefficients' or 'map'. The general supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[_kick][_filled]. For example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom, llg. The 'map_type' parser will automatically recognize which map is requested. - The program creates as many files with CCP4 or X-plor formatted maps as is requested, and it creates only one MTZ formatted file with all Fourier map coefficients in it. - The CCP4 or X-plor formatted maps can be computed in the entire unit cell or around selected atoms only. - Kick maps and missing Fobs filling is done (if requested) as described in Adams et al. (2010). Acta Cryst. D66, 213-221. - Twinning (if detected) will be accounted for automatically. This can be disabled by using "skip_twin_detection=True" keyword. - All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask, m, D, etc., can be output into a CNS or MTZ formatted reflection file. - For those who likes to experiment: bulk solvent correction and anisotropic scaling can be turned off, the data can be filtered by sigma and resolution. - For some map types certain 'map_coefficients' or 'map' scope parameters may not be applicable. For example, for "map_type=anomalous" the keywords "kicked", "fill_missing_f_obs" and some other are not applicable. - For LLG map calculation, if you specify the wavelength any existing heavy atoms (P or heavier) will be modeled as anomalous scatterers using the theoretical values of f' and f''. sømaps { map_coefficients { map_type = 2mFo-DFc format = *mtz phs mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = False } map_coefficients { map_type = 2mFo-DFc format = *mtz phs mtz_label_amplitudes = 2FOFCWT_fill mtz_label_phases = PH2FOFCWT_fill fill_missing_f_obs = True } map_coefficients { map_type = mFo-DFc format = *mtz phs mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT fill_missing_f_obs = False } map_coefficients { map_type = anomalous format = *mtz phs mtz_label_amplitudes = ANOM mtz_label_phases = PHANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = False grid_resolution_factor = 1/4. } } cC sV|jj}d}x”|t|ƒkr¨||}|jdkrM||=qntj|jƒjr›t|_ t|_ d|_ d|_ t|_ d|_n|d7}qW|jj}d}x”|t|ƒkrQ||}|jdkrö||=q¾ntj|jƒjrDt|_ t|_ d|_ d|_ t|_ d|_n|d7}q¾WdS(Nig@gð?i(tmapstmap_coefficientstlentmap_typetNonetmmtbxt map_namest anomaloustFalsetkickedtfill_missing_f_obstacentrics_scaletcentrics_pre_scalet sharpeningtsharpening_b_factortmap(tparamstmcptitmcp_tmptmp_((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pytanalyze_input_params„s<                c.C s• |tIJ|ddIJtjjƒ}t|ƒdks[t|ƒdkr+|ddkr+t|ƒdkoz|ddksàd}|d|tjjdƒfIJtjj|ƒrÎd }t ||ƒ‚nt |d ƒ}n|}|d IJ|j t j jtƒƒ}|jd |d dddƒdStjjd|d|d|ƒ}|j} | jƒ} | jjj} t| jjƒdkrÝt| jjƒdkrÝ|dIJ|j d| t j jtƒgƒ} | jƒ} n| dksï|rd| jj_ntd| ƒt|jƒdk} t|jƒdkrGt dƒ‚n| jjjdkrŠt|jƒdkrŠ|jd| jj_ntjjt| jjjƒƒsÍt dt| jjjƒƒ‚n| jjj j!dkr1| jjj j"j!dkr1t|j#ƒdkr1|j#d| jjj _!n|dI| jjjIJ|j$d| ƒ} |ddIJ|dIJ| jd |d dƒt j%jd| jjjƒ} | j&ƒg}g}x‹| jjj j!| jjj j"j!gD]b}tjjt|ƒƒråy|j't(j)|ƒƒWqGt*k r3‚qGt+k rCqGXqåqåWd}yt,j-d|d|ƒ}Wn<t.k r«}dt|ƒkr¬t dd d!ƒ‚q¬nXg}g}x‚| jjj j!| jjj j"j!gD]Y}tjjt|ƒƒrà||krà|j't/j0d|d"t1ƒƒ|j'|ƒqàqàWt2j3d#|d$t4d%|d&|ƒ}tjj5d'd(ƒ}|jj6d)ƒ}|j |ƒjƒj }tjj7d*|d+|d,d)d-d.d/d0d1t4d|ƒ}|j8}|j"}|j9}|dkr3|j:d2t;j<|j=ƒj>ƒt1ƒƒ}d}n|ddIJ|d3I| jjjIJ| j?d4t4ƒ}|j@ƒ}| jAd#|ƒ}| jjBjCdk rñ|jCd5| jjBjCƒ} | }!|jDd6|!ƒ}|jD|!ƒ}|j@ƒ}ntjjEd7| jjFd8|d9|jGƒd|ƒ| jjHdk rx| jjFd:krYt d;d<ƒ‚n|jId=| jjHd>d?ƒn|jJd@|d dAƒ|ddIJ|dBIJtjjKdC|gd7| jjFdD|dE|dF| jjj jLdG| jjMdH| jjNdI| jjOƒ}"|"jPƒ}#|#jQd |ƒ|ddIJ|dJIJ| jjjRdk rŽ|rŽtjjS| jjjRƒs|t.‚| jjjR}$n tjTƒ}$| jjjUdk rÜtjjV|$tjjW| jjjUƒƒ}%n:| jjj}%|%jXdƒdkr |%|%jYdƒ }%ntjjZdK|"d| jjdL|dMddN|%dO|ƒ}&tjj[dK|"d| jjdO|d|ƒ}'|%dP}(d})| jjj\r° |"j"ƒj]ƒ})n|'j^d|(dE|)ƒ}*| jjjdk r= |%dQ| jjj}+|dR|+IJt |+d ƒ},|"j_d |,dS| jjjƒ|,j`ƒn|dTIJ|*r^ |dU|(IJnx|&D]}-|dV|-IJqe W|ddIJ|(|&fS(WNt-iOiitNO_PARAMETER_FILEs maps.paramss;Creating parameter file '%s' in the following directory: %st.sGFile '%s' exists already. Re-name it or move and run the command again.tws All phenix.maps parameters:: touttprefixt t expert_leveltargstlogt master_paramss0No map input specified - using default map typestsourcesRs(Only one model file is allowed as input.sBmodel file is not given: maps.input.pdb_file_name=%s is not a filesFORMAT:t python_objects Parameters to compute maps:: t file_nametfrom_coordinate_filestfrom_reflection_filess.No unit cell and symmetry information supplieds:Missing or incomplete symmetry information. This program s>will only work with reflection file formats that contain both s5unit cell and space group records, such as MTZ files.tensure_read_accesstcrystal_symmetrytforce_symmetrytreflection_filesterrtmaster_scope_nametreflection_datasmaps.input.reflection_datatreflection_file_servert parameterstdata_parameter_scopetflags_parameter_scopes'maps.input.reflection_data.r_free_flagstdata_descriptionsReflection datat keep_goingtdatas Input model file:tset_atom_i_seqtstringt selectiontscattering_tabletxray_structuretd_mintneutrons4Wavelength parameter not supported when the neutron sscattering table is used.tphotonttabletsasakitfs s0Bulk solvent correction and anisotropic scaling:txray_structurestf_obst r_free_flagstoutliers_rejectiontskip_twin_detectiontbulk_solvent_correctiontanisotropic_scalings Compute maps.tfmodeltatom_selection_managertfile_name_prefixtfile_name_baset pdb_hierarchys_map_coeffs.mtzs_fmodel.s7Writing fmodel arrays (Fobs, Fcalc, m, ...) to %s file.tformats All done.sMap coefficients: %ssCCP4 or XPLOR map: %s(atlegendR Rtmaps_including_IO_master_paramsR tostpathtabspathtisfileRtopentfetchtiotbxtphiltparsetdefault_paramstshowtutilstprocess_command_line_argsRtextracttoutputtfmodel_data_file_formatR RR Rtphil_file_namestpdb_file_namestinputt pdb_file_nametstrR5R,RJtreflection_file_namesRTtpdbtcrystal_symmetry_from_cryst1tappendRt extract_fromtKeyboardInterruptt RuntimeErrorRtselect_crystal_symmetrytAssertionErrorRtany_reflection_fileRRR6tTruetdata_and_flags_master_paramstgettdetermine_data_and_flagsRIttest_flag_valuetarrayRtboolR<tsizetconstruct_hierarchytatom_selection_cachetxray_structure_simpletomitR?tselecttsetup_scattering_dictionariesR@RBt wavelengthtset_inelastic_form_factorst show_summaryt fmodel_simpleRKRLRMRNtinfot$show_rfactors_targets_scales_overallt directorytisdirtgetcwdR$tjointbasenametcounttindextcompute_xplor_mapstcompute_map_coefficientstinclude_r_free_flagstaverage_bijvoet_matestwrite_mtz_filetexporttclose(.R'R(tuse_output_directorytsuppress_fmodel_outputR)tparameter_file_nametmsgtpfotprocessed_argst working_philRRfthave_phil_file_inputtpdb_inptcs_from_coordinate_filestcs_from_reflection_filestrfnR0teR2RlR6treflection_data_master_paramstreflection_data_input_paramstreflection_data_paramstdetermine_data_and_flags_resultRIRJRzRSRPRAtomit_selectiontkeep_selectionROt fmodel_infot output_dirRRt xplor_mapstcmotmap_coeff_file_nametr_free_flags_outputtwrite_mtz_file_resulttfmodel_file_nametfmodel_file_objectR,((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pytrun¦s~ 4"     0   !     $            *                    !  !           tlaunchercB seZd„ZRS(c C sKtj|jƒtj|jƒtdt|jƒdtjdt dt ƒS(NR'R(R˜R™( RWtmkdirR¬tchdirR´tlistR'tsyststdoutRRv(tself((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pyR´us  (t__name__t __module__R´(((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pyRµtscC sM|jjjdkr$tdƒ‚nÞ|jjjjdkrKtdƒ‚n·|jjjjdkrrtdƒ‚nt|jj ƒdkr±t|jj ƒdkr±tdƒ‚nQ|jj j dk rt jj|jj j ƒ rtdd|jj j ƒ‚n|jjdk r<|jjdkr<td d ƒ‚q<nt|jƒtS( NsNo model file defined.sNo reflection file defined.s%No labels chosen for reflection data.is+You have not requested any maps for output.s8The output directory %s does not exist; please choose a s/valid directory, or leave this parameter blank.RCs4Wavelength parameter not supported when the neutron sscattering table is used.(RRiRjR RR5R,tlabelsR RR ReRŠRWRXR‹R„R@tvalidate_map_paramsRv(Rtcallback((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pytvalidate_params}s&0 c C sMddlm}g}xè|jD]Ý}|jdk r y||jƒ}Wn%tk ro}tt|ƒƒ‚nX|j}|j }||ksš||kr¿tdddd||fƒ‚n(d||gkrçtd|jƒ‚n|j ||gƒq q Wt |dƒrIx6|j D](}|j d krtd d ƒ‚qqWntS( Niÿÿÿÿ(Rs8The map coefficients with MTZ labels %s,%s duplicates atsC least one previously defined label. You may output multiple sets sCof coefficients with the same map type, but the column labels must s be unique.s8Please specify both MTZ column labels for map_type '%s'.Rgà?s4The grid resolution factor for CCP4 and X-PLOR maps smust be 0.5 or less.(R RR R R RrRRktmtz_label_amplitudestmtz_label_phasestextendthasattrRtgrid_resolution_factorRv( RRR¾t map_coeffst decode_mapR¤RGtphiR((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pyR¿—s0   cC s‰|\}}g}|dk rFtjj|ƒrF|j|dfƒnx6|D].}tjj|ƒrM|j|dfƒqMqMW|gfS(NsMTZ files XPLOR map(R RWRXRZRo(tresultstmtz_filet map_filest output_filestmap_file((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pyt finish_job³s  t__main__R'i(&t __future__Rt mmtbx.mapsR tscitbx.array_familyRRWR¹trandomt iotbx.pdbR]t libtbx.utilsRtlibtbxRt mmtbx.utilsRRRtcctbxRtseedtset_random_seedRUR`RRºRvRR´ttarget_with_save_resultRµR RÁR¿RÏR¼targv(((sE/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/maps.pyts0 $    L% "  Í