ó ©%Tc@soddlZddlZddlZddlZd„ZerkejƒrcedƒZ e rse e dd„ƒnd„Z edƒZ ej ƒZ ejdƒZej ƒZejd ƒZej ƒZejd ƒZej ƒZejd ƒZej ƒZejd ƒZej ƒZejd ƒZej ƒZejdƒZej ƒZejdƒZej ƒZejdƒZej ƒZ ejdƒZ!ej"e ƒe j#eƒej$ƒej"eƒe j#eƒej$ƒej"eƒe j#eƒej$ƒe!j"e ƒe j#e!ƒe!j$ƒej"eƒe j#eƒej$ƒej"eƒe j#eƒej$ƒej"eƒe j#eƒej$ƒej"eƒe j#eƒej$ƒej"eƒe j#eƒej$ƒej"eƒe j#eƒej$ƒe e dd„ƒd„Z%e e dd„ƒd„Z&e e dd„ƒd„Z'e e dd„ƒd„Z(d„Z)d„Z*d „Z+e ed!d"„ƒe ed#d$„ƒe ed%d&„ƒe ed'd(„ƒe ed)d*„ƒe ed+d,„ƒd-„Z,e ed.d/„ƒe ed0d1„ƒd2„Z-e ed3d4„ƒe ed5d6„ƒe ed7d8„ƒd9„Z.e ed:d;„ƒe ed<d=„ƒe ed>d?„ƒe ed@dA„ƒe edBdC„ƒe edDdE„ƒe edFdG„ƒe edHdI„ƒej ƒZ/ejdJƒZ0e0j"e/ƒe j#e0ƒe0j$ƒe e/dJdK„ƒdL„Z1e e/dMdN„ƒej ƒZ/ejdOƒZ0e0j"e/ƒej#e0ƒe0j$ƒe e/dPdQ„ƒe e/dRdS„ƒdT„Z2e edUdV„ƒe edWdX„ƒdY„Z3e edZd[„ƒe ed\d]„ƒd^„Z4e ed_d`„ƒe edadb„ƒdc„Z5e eddde„ƒdfdg„Z6e edhdi„ƒdj„Z7e edkdl„ƒdm„Z8e edndo„ƒe edpdq„ƒe9drƒre edsdt„ƒne edudv„ƒe edwdx„ƒe edydz„ƒe ed{d|„ƒe ed}d~„ƒe edd€„ƒe edd‚„ƒe edƒd„„ƒe ed…d†„ƒe ed‡dˆ„ƒe ed‰dŠ„ƒe ed‹dŒ„ƒe eddŽ„ƒej ƒZ/ejdƒZ0e0j"e/ƒej#e0ƒe0j$ƒe e/dd‘„ƒe e/d’d“„ƒe ed”d•„ƒd–„Z:e ed—d˜„ƒe ed™dš„ƒd›„Z;e e dœd„ƒdž„Z<e e dŸd „ƒd¡„Z=e e d¢d£„ƒe e d¤d¥„ƒej ƒZ/ejd¦ƒZ0e0j"e/ƒe j#e0ƒej>d?krn e0j?d©ƒne@jAe0d©ƒe0j$ƒe e/dªd«„ƒe e/d¬d­„ƒe e/d®d¯„ƒe ed°d±„ƒej ƒZ/ejd²ƒZ0e0j"e/ƒej#e0ƒe0j$ƒd³„ZBe e/d´dµ„ƒd¶„ZCe e/d·d¸„ƒd¹„ZDe edºd»„ƒe ed¼d½„ƒej ƒZ/ejd¾ƒZ0e0j"e/ƒej#e0ƒe0j$ƒe e/d¿dÀ„ƒe e/dÁd„ƒe e/dÃdÄ„ƒe edÅdÆ„ƒe edÇdÈ„ƒe edÉdÊ„ƒdË„ZEe edÌdÍ„ƒd΄ZFe edÏdЄƒe edÑdÒ„ƒe edÓdÔ„ƒdÕ„ZGe e dÖdׄƒeHƒrK eId§krK ej ƒZJejd؃ZKeKj"eJƒe j#eKƒeKj$ƒe eJdÙdÚ„ƒe eJdÛdÜ„ƒe eJdÝdÞ„ƒe eJdßdà„ƒqK ne edád℃dã„ZLe edäd儃e edæd焃e edèd鄃dêdë„ZMe edìd턃e edîde edðdñ„ƒdò„ZNe edódô„ƒdõ„ZOe edöd÷„ƒdø„ZPe edùdú„ƒe edûdü„ƒe edýdþ„ƒej ƒZ/ejdÿƒZ0e0j"e/ƒe j#e0ƒe0j$ƒe e/dd„ƒe e/dd„ƒe e/dd„ƒe e/dd„ƒe e/dd „ƒe e/d d „ƒej ƒZ/ejd ƒZ0e0j"e/ƒej#e0ƒe0j$ƒe e/d d„ƒe e/dd„ƒe e/dd„ƒd„ZQe edd„ƒe edd„ƒe edd„ƒe edd„ƒe edd„ƒe edd„ƒe ed d!„ƒej ƒZ/ejd"ƒZ0e0j"e/ƒej#e0ƒe0j$ƒe e/d#d$„ƒe e/d%d&„ƒe ed'd(„ƒe ed)d*„ƒd+„ZRe ed,d-„ƒe ed.d/„ƒd0„ZSe ed1d2„ƒe ed3d4„ƒe ed5d6„ƒd7„ZTe ed8d9„ƒedƒZ e e d:d;„ƒe e d<d=„ƒqkd>GHndS(@iÿÿÿÿNcCs'tjƒ}|j|ƒ|jƒdS(N(tgtktMenuItemtaddtshow(tmenutsep((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytadd_coot_menu_separators  tValidatesHighly coordinated waters...cCstƒS(N(twater_coordination_gui(tfunc((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyt8scCstdƒ}tdƒdS(Nt Restraintssuser_define_restraints.py(tcoot_menubar_menutload_from_search_load_path(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyt"add_module_user_defined_restraints?s t E_xtensionssAll Molecule...sMaps...s Modelling...s Refine...tRepresentationss Settings...sPISA...sPDBe...s Modules...sNCS...s"[Post MR] Fill Partial Residues...cCstdd„ƒS(Ns)Find and Fill residues with missing atomscSs t|ƒS(N(tfill_partial_residues(timol((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ”s(tmolecule_chooser_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR “scCs3tƒdkrtdƒntat|tƒdS(Niÿÿÿÿsoops. Must set a map to fit(timol_refinement_maptadd_status_bar_texttTruetcontinue_multi_refinetinterruptible_fit_proteintfit_protein_fit_function(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytfit_protein_func1´s sFit Protein...cCstdd„ƒS(Ns Fit Protein using Rotamer SearchcSs t|ƒS(N(R(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Às(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¿scCs3tƒdkrtdƒntat|tƒdS(Niÿÿÿÿsoops. Must set a map to fit(RRRRRt#fit_protein_stepped_refine_function(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytfit_protein_func2Ãs sStepped Refine...cCstdd„ƒS(Ns'Fit Protein using Real-Space RefinementcSs t|ƒS(N(R(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ïs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÎscCs3tƒdkrtdƒntat|tƒdS(Niÿÿÿÿsoops. Must set a map to fit(RRRRRtfit_protein_rama_fit_function(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytfit_protein_func3Òs s#Refine/Improve Ramachandran Plot...cCstdd„ƒS(Ns3Refine Protein with Ramachanran Plot Optimization: cSs t|ƒS(N(R(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Þs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÝscCsod}tƒ}|gks`xM|D]7}t||ƒr"d||GHt||ƒ}Pq"q"Wn dGHt}|S(Nts%s is a valid map molecules,BL WARNING:: dunno what to do!? No map found(tmolecule_number_listtis_valid_map_moleculetstrtFalse(tft molecule_listti((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyt mask_map_funcæs     cCs dG|GHdS(Nschanged active_state to ((t active_state((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytmask_map_func1ôsc CsÇ|d}|d}|d}t}yt|ƒ}t}Wnd|GHnX|rÃ|rbd}nd}dG|GH|dkr­yt|ƒ} t| ƒWq­d|GHq­Xnt||||ƒndS(NiiisLBL WARNING:: input %s for Map molecule number is not an integer. Bailing outsdebug:: invert-mask? istdefaultsCBL WARNING:: could not set map mask radius to %s. It's not a number(R#tintRtfloattset_map_mask_atom_radiustmask_map_by_atom_selection( Rt texts_listtinvert_mask_qmttext_1ttext_2ttext_3t continue_qmtntinvertt new_radius((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytmask_map_func2÷s*          cCs'tƒ}|dkrt|ƒSdSdS(NiR*(tmap_mask_atom_radiusR"(trad((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytmask_map_radius_funcs   sMask Map by Atom Selection...cCstdd„ƒS(Ns2Define the molecule that has atoms to mask the mapcsFtdtƒgddgdtƒggdd„gd‡fd†ƒS( Ns Map molecule number: s Atom selection: s//A/1sRadius around atoms: s Invert Masking? cSs t|ƒS(N(R)(R(((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR #ss Mask Map cstˆ||ƒS(N(R8(t text_listR6(R(sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR $s(t*generic_multiple_entries_with_check_buttonR'R;(R((RsQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR s    (R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssCopy Map Molecule...cCstdd„ƒS(NsMap to Copy...cSs t|ƒS(N(t copy_molecule(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR +s(tmap_molecule_chooser_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR *ssMake a Difference Map...cCstƒS(N(tmake_difference_map_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 1ss!Transform map by LSQ model fit...cCstƒS(N(t"transform_map_using_lsq_matrix_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 7ssAverage Maps...cCstƒS(N(taverage_map_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR =ss Export map...cCstdtddd„ƒS(Ns Export Map: s File_name: RcSs1t||ƒdko0tdt|ƒd|ƒS(NisMap s exported to (t export_mapRR"(Rttext((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ds(t!generic_chooser_and_file_selectortvalid_map_molecule_qm(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Bs cCsZd}yt|ƒ}Wnd|GHnX|dkrVt|gtƒ||gŒndS(Ngð¿s%BL WARNING:: radius %s was no number!i(R,texport_map_fragmenttrotation_centre(Rt radius_stringt file_nametradius((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytexport_map_funcHs  sExport Local Map Fragment...cCstdtdddd„ƒS(Ns Export Map: s Radius (A): t10s File-name: cSst|||ƒS(N(RL(RRIRJ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Zs(t'generic_chooser_entry_and_file_selectorRF(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Us s Brighten MapscCstƒS(N(t brighten_maps(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR cscCsd|GHt|ƒdS(Ns,setting map number %s to be a difference map(tset_map_is_difference_map(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytset_diff_map_funcfs sSet map is a difference map...cCstdd„ƒS(Ns0Which map should be considered a difference map?cSs t|ƒS(N(RQ(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ns(R?(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR mssAnother (contour) level...cCstƒS(N(t another_level(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR tssMulti-chicken...cCstdd„ƒS(Ns)Choose a molecule for multiple contouringcSst|dƒt|ƒfS(Ni(tset_map_displayedt multi_chicken(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR {s(R?(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR zsc Cs2tƒ#\}}}}}}t|ƒWdQXdS(N(tUsingActiveAtomtadd_hydrogens_using_refmac(taa_imolt aa_chain_idt aa_res_not aa_ins_codet aa_atom_namet aa_alt_conf((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytadd_hydrogens_refmac_funcƒs sAdd Hydrogens using RefmaccCstƒS(N(R](R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ‹ssAdd Other Solvent Molecules...cCstƒS(N(tsolvent_ligands_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ‘ss Arrange Waters Around Protein...cCstdd„ƒS(NsArrange waters in molecule: cSs t|ƒS(N(tmove_waters_to_around_protein(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ™s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR —ss'Assign (force) HETATMs for this ResiduecCsttddddƒS(NRWRXRYRZ(tusing_active_atomthetify_residue(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ŸssAssign HETATM to molecule...cCstdd„ƒS(Ns$Assign HETATMs as per PDB definitioncSs t|ƒS(N(tassign_hetatms(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR §s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¦ssCopy Coordinates Molecule...cCstdd„ƒS(NsMolecule to Copy...cSs t|ƒS(N(R>(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ®s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ­ssCopy Fragment...cCstdddd„ƒS(Ns[Create a new Molecule From which molecule shall we seed?sAtom selection for fragments//A/1-10cSs t||ƒS(N(tnew_molecule_by_atom_selection(RRD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ·s(tgeneric_chooser_and_entry(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ´ss DB Loop...cCstƒS(N(tclick_protein_db_loop_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¿ssDock Sequence...cCstƒS(N(tcootaneer_gui_bl(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ísc Cs›ddl}ddl}d}|jd|jƒ}dG|G|G|GH|jj|ƒrŽt|dƒ}|jƒ}|jƒt |||ƒn dG|GHdS(Niÿÿÿÿitchains assoc seq:trsBL WARNING:: could not find( tostretcompilet IGNORECASEtpathtisfiletopentreadtclosetassign_pir_sequence( Rtchain_idtpir_fileRiRjt chain_countt reg_chaintfintseq_text((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytassociate_seq_funcÐs  sAssociate Sequence to Chain...cCstƒS(N(t!associate_sequence_with_chain_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR þssFind Secondary Structure...s Find HelicescCstƒS(N(t find_helices(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ss Find StrandscCstƒS(N(t find_strands(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR sc CsGtƒ8\}}}}}}t||||ƒ}t|ƒWdQXdS(N(RUt residue_namet get_SMILES_for_comp_id_from_pdbe(RWRXRYRZR[R\tcomp_id((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytget_smiles_pdbe_funcs  sFetch PDBe ligand descriptioncCstƒS(N(R€(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssFix Nomenclature Errors...cCstdd„ƒS(Ns#Fix Nomenclature Error in molecule:cSs t|ƒS(N(tfix_nomenclature_errors(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR &s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR %sc Cs>tƒ/\}}}}}}t|||||ƒWdQXdS(N(RUtinvert_chiral_centre(RWRXRYRZR[R\((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytchiral_centre_inverter_func+s  sInvert This Chiral CentrecCstƒS(N(Rƒ(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 4ssJLigand launchcCstƒS(N(tlaunch_jligand_function(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR =scGsn|d}|d}t|ƒ}t|ƒ}|d}|d}||ksTdGHnt|||ddƒdS(NiiisMismatch moleculestdummygš™™™™™¹?(tatom_spec2imolt make_link(targstm_spec_1tm_spec_2timol_1timol_2tspec_1tspec_2((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytmake_link_ext_funcCs       sMake Link (click 2 atoms)...cCs tdtƒS(Ni(tuser_defined_clickR(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR RssMerge Water Chains...cCstdd„ƒS(NsMerge Water Chains in molecule:cSs t|ƒS(N(tmerge_solvent_chains(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Zs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR YscCs2d}t||ƒ}t|ƒs.t|ƒndS(Ni(tget_monomer_from_dictionarytvalid_model_molecule_qmt get_monomer(RDt idealizedt new_model((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyt mon_dict_func]s sMonomer from DictionarycCstdddd„ƒS(Ns7Pull coordinates from CIF dictionary for 3-letter-code:Rs Get Coords cSs t|ƒS(N(R—(RD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR is(tgeneric_single_entry(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR fs ic Cs8tƒ)\}}}}}}t|||ƒWdQXdS(N(RUtmorph_fit_chain(RKRWRXRYRZR[R\((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytmorph_fit_chain_funcls sMorph Fit Chain (Radius 7)cCstƒS(N(Rš(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR tscCsKyt|ƒ}WndG|GHnX|gtƒ|dg}t|ŒdS(NsWARNING:: no valid radiusi(R,RHt new_molecule_by_sphere_selection(RRDRKRˆ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytnew_mol_sphere_func1ys  sNew Molecule by Sphere...cCstdddd„ƒS(Ns9Choose a molecule from which to select a sphere of atoms:sRadius:s10.0cSs t||ƒS(N(Rœ(RRD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ‡s(Rd(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR „scCs\ddlm}t|ƒ}t|ƒ|k r6dGHn"t|||d|d|dƒdS(Niÿÿÿÿ(tListTypesbad pre-shift abortingiii(ttypesRtorigin_pre_shiftttypetnew_molecule_by_symop(RRDRt pre_shift((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytnew_mol_sym_func1Šs  s New Molecule from Symmetry Op...cCstdddd„ƒS(Ns/Molecule from which to generate a symmetry copytSymOpsX,Y,ZcSs t||ƒS(N(R£(RRD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ›s(Rd(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ˜ssPhosphorylate this residuecCstƒS(N(tphosphorylate_active_residue(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR £stcprodrgs-Prodrg-ify this residue (generate restraints)cCsttddddƒS(NRWRXRYRZ(R`t prodrg_ify(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR «ssRename Residue...cCstƒS(N(trename_residue_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¶ssRenumber Waters...cCstdd„ƒS(Ns"Renumber waters of which molecule?cSs t|ƒS(N(trenumber_waters(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¾s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¼ssReorder Chains...cCstdd„ƒS(NsSort Chain IDs in molecule:cSs t|ƒS(N(t sort_chains(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Æs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÅssReplace Fragment...cCstdd„ƒS(Ns'Define the molecule that needs updatingcstddd‡fd†ƒS(Ns(Molecule that contains the new fragment:sAtom Selections//cstˆ||ƒS(N(treplace_fragment(t imol_fragmenttatom_selection_str(t imol_base(sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Òs(Rd(R®((R®sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ïs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÎssReplace Residue...cCstdddd„ƒS(Ns*Replace this residue with residue of type:tALAtMutatecSsttddd|ƒS(NRWRXRY(R`tmutate_by_overlap(RD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ûs (R˜(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÙssResidue Type Selection...cCstdddd„ƒS(Ns+Choose a molecule to select residues from: s Residue Type:RcSst||ƒtƒfS(N(t&new_molecule_by_residue_type_selectiont#update_go_to_atom_window_on_new_mol(RRD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ås (Rd(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR äs sResidues with Alt Confs...cCstdd„ƒS(Ns&Which molecule to check for Alt Confs?cSs t|ƒS(N(t alt_confs_gui(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR îs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ìss"Residues with Cis Peptide Bonds...cCstdd„ƒS(Ns/Choose a molecule for checking for Cis PeptidescSs t|ƒS(N(tcis_peptides_gui(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR õs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ôssResidues with Missing Atoms...cCstdd„ƒS(Ns*Which molecule to check for Missing Atoms?cSs t|ƒS(N(tmissing_atoms_gui(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ýs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ûss Rigid Body Fit Residue Ranges...cCstd„ddƒS(NcSs t||ƒS(N(t#rigid_body_refine_by_residue_ranges(Rtls((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssRigid Body Refines Fit (tresidue_range_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR s sRigid Body Fit Molecule...cCstdd„ƒS(NsRigid Body Fit MoleculecSs t|dƒS(Ns//(t#rigid_body_refine_by_atom_selection(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssSuperpose ligandscCstƒS(N(tsuperpose_ligand_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssSymm Shift Reference Chain HerecCstƒS(N(t+move_reference_chain_to_symm_chain_position(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssRotamer Search...sUse "Backrub" RotamerscCs ttƒS(N(tset_rotamer_search_modetROTAMERSEARCHLOWRES(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR )ssDONT use "Backrub" RotamerscCs ttƒS(N(R½tROTAMERSEARCHHIGHRES(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR /ss Use SEGIDs...cCstdd„ƒS(Ns,Exchange the Chain IDs, replace with SEG IDscSs t|ƒS(N(texchange_chain_ids_for_seg_ids(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 7s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 6scCsutƒ}t|dd!Œ}|d}t|ƒ}t|tƒradt|ƒd|d|nd}t|ƒdS(Niis (mol. no: s) s: s (tactive_residueR}t comp_id2namet isinstanceR"R(tcentral_residuetres_nametmol_noR5ts((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyt whats_this<s    5s What's this?cCstƒS(N(RÈ(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR IssAtoms with Zero Occupancies...cCstdd„ƒS(Ns8Which molecule to check for Atoms with zero occupancies?cSs t|ƒS(N(tzero_occ_atoms_gui(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ss(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR QscCsBy/t|ƒ}t|ƒ}t||||ƒWn dGHnXdS(Ns"BL WARNING:: no valid number input(R+t,copy_residue_range_from_ncs_master_to_others(RRsttext1ttext2tr1tr2((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytcopy_ncs_range_func[s   sCopy NCS Residue Range...cCstddtƒd„ƒS(NsApply NCS Range from MastersMaster Chain IDc s+tddddttd‡‡fd†ƒS(NsStart of Residue Number RangesEnd of Residue Number RangeRsApply NCS Residue Rangecstˆˆ||ƒS(N(RÏ(RËRÌ(RsR(sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ms(tgeneric_double_entryR#(RRs((RsRsQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR is (Rdtget_first_ncs_master_chain(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR fscCs@t|ƒ}|r"t||ƒndt|ƒ}t|ƒdS(Ns.You need to define NCS operators for molecule (t ncs_chain_idstcopy_from_ncs_master_to_othersR"t info_dialog(RRst ncs_chainsRÇ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytcopy_ncs_chain_funcps  sCopy NCS Chain...cCstddtƒd„ƒS(Ns5Apply NCS edits from NCS Master Chain to Other ChainssMaster Chain IDcSs t||ƒS(N(RÖ(RRs((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ~s(RdRÑ(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR {sc scddlm‰d}d}d}d}d}‡‡fd†}t||||tt||ƒdS( Niÿÿÿÿ(RsStart ResNumbers End ResNumberRMt20sRegenerate Ghostscs‚t}y"t|ƒ}t|ƒ}t}Wn dGHnX|r~tˆƒ}t|ƒˆkr~|d}tˆ|||ƒq~ndS(Ns6BL WARNING:: input residue numbers have to be integersi(R#R+RRÒR tmanual_ncs_ghosts(t resno_1_textt resno_2_texttconttresno_1tresno_2tghost_ncs_chain_idstghost_chain_list(RR(sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pythandle_go_functionˆs      (RžRRÐR#(Rtlabel_1tlabel_2tentry_1_default_texttentry_2_default_texttgo_button_labelRà((RRsQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytncs_ghost_res_range_funcs  sNCS Ghosts by Residue Range...cCstdd„ƒS(Ns#Make local NCS ghosts for molecule:cSs t|ƒS(N(Ræ(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¢s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¡ssNCS ligands...cCstƒS(N(tncs_ligand_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¨ssNCS matrix type...ii s2use to change the way the NCS matrix is calculatedsAccurate (SSM)cCs tdƒS(Ni(tset_ncs_matrix_type(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¹ss Fast (LSQ)cCs tdƒS(Ni(Rè(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¿ss#Extra Fast (LSQ, only every 2nd CA)cCs tdƒS(Ni(Rè(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÅssSet Refinement Options...cCstƒS(N(trefinement_options_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÐssPeptide Restraints...cCsdGHtƒdS(NsPlanar Peptide Restraints added(tadd_planar_peptide_restraints(((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytadd_restr_func1ÙssAdd Planar Peptide RestraintscCstƒS(N(Rë(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR àscCsdGHtƒdS(Ns!Planar Peptide Restraints removed(t remove_planar_peptide_restraints(((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytadd_restr_func2ãss Remove Planar Peptide RestraintscCstƒS(N(Rí(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ésc sAtjtjƒ‰tjtdƒ}tjtdƒ}tjdƒ}tjdƒ}d}d}tjƒ}ˆj|ƒt ||ƒ‰t ||ƒ‰‡fd†}‡‡‡fd†}|j d|ƒ|j d|ƒ|j |ttd ƒ|j |ttd ƒ|j |t tdƒ|j |t tdƒˆjƒdS( Nis Refine s Cancel s,HKL data filename (leave blank for default)s' Choose molecule for SHELX refinement csˆjƒtS(N(tdestroyR#(Rˆ(twindow(sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytshelx_delete_eventús cspddl}ˆjƒ}tˆŒ}|j|ƒrbt|ƒdkrRt|ƒqbt||ƒnˆjƒtS(Niÿÿÿÿi(toperatortget_texttget_option_menu_active_moleculet isNumberTypetlent shelxl_refineRîR#(RˆRñttxtR(tentrytoption_menu_mol_list_pairRï(sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytshelx_go_funcn_eventþs     tclickedi(RtWindowtWINDOW_TOPLEVELtVBoxR#tHBoxtButtont HSeparatorRtgeneric_molecule_choosertfile_selector_entrytconnectt pack_startRtshow_all( tvboxthboxt go_buttont cancel_buttontentry_hint_texttchooser_hint_textth_sepRðRú((RøRùRïsQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytshelx_ref_funcìs(   sSHELXL Refine...cCstƒS(N(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssRead REFMAC logfile...cCstdtddd„ƒS(NsRead Refmac log filesLogfile name: RcSs t||ƒS(N(tread_refmac_log(RRD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR s(RER“(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR s sRefinement Speed...sMolasses Refinement modecCstdƒtdƒfS(Ns Molasses...i(tprintft&set_dragged_refinement_steps_per_frame(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR -s sCrocodile Refinement modecCstdƒtdƒfS(NsCrock...i (RR(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 4s s!Normal Refinement mode (1 Emsley)cCstdƒtdƒfS(NsDefault Speed (1 Emsley)...iP(RR(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ;s sAuto-weight refinementcCstƒS(N(tauto_weight_for_refinement(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR BssSet Undo Molecule...cCstdd„ƒS(Ns&Set the Molecule for 'Undo' OperationscSs t|ƒS(N(tset_undo_molecule(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Is(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR HssB factor bonds scale factor...cCstdddd„ƒS(Ns@Choose a molecule to which the B-factor colour scale is applied:sB-factor scale:s1.0cSst|t|ƒƒS(N(tset_b_factor_bonds_scale_factorR,(RRD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Rs(Rd(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR PscCsVddl}t|ƒ}|j|ƒrHd|}t|ƒt|ƒn tdƒdS(NiÿÿÿÿsMatrix set to sFailed to read a number(RñR,Rôt set_matrixR(RDRñttRÇ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyt set_mat_funcUs     s!Set Matrix (Refinement Weight)...cCstdttƒƒdd„ƒS(Ns+set matrix: (smaller means better geometry)sSet itcSs t|ƒS(N(R(RD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ds(R˜R"t matrix_state(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR bscCsVddl}t|ƒ}|j|ƒrHd|}t|ƒt|ƒn tdƒdS(Niÿÿÿÿs Density Fit scale factor set to sFailed to read a number(RñR,Rôt$set_residue_density_fit_scale_factorR(RDRñRRÇ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytset_den_gra_funcgs     sSet Density Fit Graph Weight...cCs#tdtdtƒƒdd„ƒS(Ns0set weight (smaller means apparently better fit)s%.2fsSet itcSs t|ƒS(N(R(RD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR vs(R˜R"t residue_density_fit_scale_factor(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR tssPDBe recent structures...cCstƒS(N(tpdbe_latest_releases_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssGet from PDBe...cCstdddd„ƒS(NsGet PDBe accession codeRs Get it cSstd|jƒƒS(Ns include-sfs(tpdbe_get_pdb_and_sfs_ciftrstrip(RD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR …s(R˜(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ƒscCst}tjdƒ}|s'tƒ}ntjj|ddƒ}tjj|ƒritjj|dƒ}n|rtjj|dƒ}tjj|dƒ}tjj|ƒr¸t|ƒntjj|ƒrt |ddd d d ƒt |d d d d d ƒqndS(Nt COOT_PREFIXtsharetcoottdatastutorial-modern.pdbsrnasa-1.8-all_refmac1.mtztFWTtPHWTRitDELFWTtPHDELWTi( R#Ritgetenvt pkgdatadirRmtjointisdirRntread_pdbtmake_and_draw_map(tdata_dirt prefix_dirt pkg_data_dirt pdb_file_namet mtz_file_name((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytload_tutorial_data_funcŒs  sLoad tutorial model and datacCstƒS(N(R2(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¢ssLidia...sHydrogenate regioncCs tdƒS(Ni(thydrogenate_region(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR »ss View in LIDIAcCsttddddƒS(NRWRXRYRZ(R`tfle_view(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÃssLoad SBase monomer...cCstdddd„ƒS(Ns+Load SBase Monomer from three-letter-code: Rs Load cSs t|ƒS(N(tget_sbase_monomer(ttlc((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ðs(R˜(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÌssActivate prodrg flat modecCsttdddƒS(NRWRXRY(R`t prodrg_flat(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ×ssUndo Symmetry ViewcCstƒS(N(tundo_symmetry_view(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR æscCs%t||dddƒ}dG|GHdS(Ng ×£p= Ç?g333333Ó?ishandle: (tmake_ball_and_stick(RRDt bns_handle((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytmake_ball_n_stick_funcéssBall & Stick...cCstddtd„ƒS(Ns Ball & SticksAtom Selection:cSs t||ƒS(N(R;(RRD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ôs(Rdt default_ball_and_stick_selection(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ñssClear Ball & Stick...cCstdd„ƒS(Ns8Choose a molecule from which to clear Ball&Stick objectscSs t|ƒS(N(tclear_ball_and_stick(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR üs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ússElectrostatic Surface...cCstdddd„ƒS(Ns.Choose a molecule to represent as a surface...s s Can be SLOWcSs t|dƒS(Ni(t do_surface(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR s(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR sic Csétƒ}|d}|d}|d}|d}|d}|d}tƒ}t||dd!dƒ} g} x3| D]+} t|| Œdkrt| j| ƒqtqtWt|ƒ} t| |||ƒ|rØt| | ƒn t| dƒdS( 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save_views(R÷((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ›s(R˜(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ™ss3D Annotations...sAnnotate position...cCstdddd„ƒS(Ns Annotation: RsMake AnnotationcSs t|ƒS(N(tadd_annotation_here(R÷((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ®s(R˜(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¬s sSave Annotations...cCstdddd„ƒS(NsSave Annotationsscoot_annotations.pys Save cSs t|ƒS(N(tsave_annotations(RJ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¸s(R˜(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR µssLoad Annotations...cCstdddd„ƒS(NsLoad Annotationsscoot_annotations.pys Load cSs t|ƒS(N(tload_annotations(RJ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR Ás(R˜(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ¾scCsœddl}d}t|ƒ|jdkr4d}nd}t|ƒrt|dƒ}|jj|ƒ}|d|g}|j|j||ƒn d|GHdS( Niÿÿÿÿs 1.mgpic.pytnts winccp4mg.exetccp4mgtPATHs-picts*BL WARNING:: sorry cannot find %s in $PATH( Rit write_ccp4mg_picture_descriptiontnametcommand_in_path_qmtfind_exeRmtabspathtspawnvtP_NOWAIT(Rit pd_file_namet ccp4mg_exetccp4mg_file_exeRˆ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyt ccp4mg_func1És    s CCP4MG...cCstƒS(N(Rs(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ÛssPISA Assemblies...cCstdd„ƒS(Ns*Choose molecule for PISA assembly analysiscSs t|ƒS(N(tpisa_assemblies(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR æs(R(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ässPISA Interfaces...cCstdd„ƒS(Ns+Choose molecule for PISA interface analysiscSs 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((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssSet Spin SpeedcCstdttƒƒdd„ƒS(Ns"Set Spin Speed (smaller is slower)sSet itcSstt|ƒƒS(N(tset_idle_function_rotate_angleR,(RD((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR !s(R˜R"tidle_function_rotate_angle(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR ssNudge Centre...cCstƒS(N(tnudge_screen_centre_gui(R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR &scCs4x-tƒD]"}t|ƒr t|dƒq q WdS(Ni(R R“tset_symmetry_whole_chain(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pytall_mol_symm_func)s s(All Molecules use "Near Chains" SymmetrycCstd„tƒƒS(NcSst|ƒot|dƒS(Ni(R“R(R((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 0s (R^R (R ((sQ/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/extensions.pyR 0s 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