# # Copyright (C) 1999-2004 Liz Potterton, Peter Briggs # # This code is distributed under the terms and conditions of the # CCP4 Program Suite Licence Agreement as a CCP4 Library. # A copy of the CCP4 licence can be obtained by writing to the # CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. # #CCP4i_cvs_Id $Id$ # ====================================================================== # pdbset.tcl -- # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------- proc pdbset_run { arrayname } { #------------------------------------------------------------------------- upvar #0 $arrayname array if { $array(NRENUMBER) > 0 } { for { set n 1 } { $n <= $array(NRENUMBER) } {incr n } { if [regexp RENAME [GetValue $arrayname EDIT_MODE,$n]] { set array(RENUMBER_MODE,$n) SAME } } } return 1 } #--------------------------------------------------------------------- proc pdbset_setup { typedefVar arrayname } { #--------------------------------------------------------------------- upvar #0 $typedefVar typedef set typedef(_pdbset_edit_mode) { menu { "Renumber residue" \ "Rename chain" } \ { RENUMBER RENAME } } set typedef(_pdbset_renumber) { menu { "starting at" "increment by" } { INIT INC } } # List of programs. Try to get unified task interface to pdbset and pdbcur set typedef(_task_prg) { menu { "pdbcur" \ "pdbset" } \ { PDBCUR PDBSET }} # This is sum of _pdbcur_action and _pdbset_action # It seems necessary to control visibility of folders set typedef(_task_action) {menu \ {"summarise contents of coordinate file" \ "remove hydrogen atoms" \ "remove alternative conformations" \ "remove atoms with low/zero occupancy" \ "remove anisotropic U's"\ "rename chains and/or renumber residues" \ "generate chains via symmetry operations" \ "transform / shift or rotate structure" \ "replace atoms or residues" \ "perform selection for output PDB file" \ "average main and side chain Bfactors" } \ { SUMMARISE DELHYD MOSTPROB CUTOCC NOANISOU \ RENAME \ SYMMETRY ROTATE REPLACE SELECT AVERAGE } } set typedef(_pdbcur_action) {menu \ {"summarise contents of coordinate file" \ "remove hydrogen atoms" \ "remove alternative conformations" \ "remove atoms with low/zero occupancy" \ "remove anisotropic U's" } \ { SUMMARISE DELHYD MOSTPROB CUTOCC NOANISOU} } set typedef(_pdbset_action) {menu \ {"rename chains and/or renumber residues" \ "generate chains via symmetry operations" \ "transform / shift or rotate structure" \ "replace atoms or residues" \ "perform selection for output PDB file" \ "average main and side chain Bfactors" } \ { RENAME SYMMETRY ROTATE \ REPLACE SELECT AVERAGE } } set typedef(_pdbset_bfactor) {menu {"All" "minimum" "maximum" \ "Range" "if 0.0" } \ { ALL MINIMUM MAXIMUM \ RANGE DEFAULT }} set typedef(_pdbset_occupancy) {menu {"All" "Minimum" "Reset" \ "if 0.0" } \ {ALWAYS MINIMUM RESET \ DEFAULT }} set typedef(_pdbset_repl_mode) { menu { "residue" \ "atom" } \ { REPLACE_RESIDUE \ REPLACE_ATOM } } set typedef(_pdbset_ncs_isfract) {menu { "orthogonal Angstroms" \ "fractional coordinates" } \ { ORTHOG FRACT }} set typedef(_pdbset_rot_type) {menu { \ "matrix definition" "euler angles" "polar angles" } \ { MATRIX EULER POLAR }} set typedef(_pdbset_ncode) {menu { \ "do not generate matrix " \ "axes along a, c* x a, c* (Brookhaven standard)" \ "axes along b, a* x b, a* " \ "axes along c, b* x c, b* " \ "axes along a + b, c* x (a+b), c* " \ "axes along a*, c x a*, c (Rollet) " \ "axes along a, b*, a x b* " \ "axes along a*, b a* x b (TNT convention) " } \ { CODE0 CODE1 CODE2 CODE3 CODE4 CODE5 CODE6 CODE7 } } set typedef(_pdbset_symgen_mode) {menu { "spacegroup" \ "individual symmetry operations" } { SYMGEN_SPACE SYMGEN_OP } } set typedef(_pdbset_trans_type) {menu {"no action" "rotation" "translational shift" "rotation and shift" } { NONE ROTATE SHIFT BOTH } } return 1 } #---------------------------------------------------------------- proc pdbset_renumber { arrayname counter } { #---------------------------------------------------------------- OpenSubFrame frame -toggle_display EDIT_MODE,$counter open RENAME CreateLine line \ message "Rename chain id and/or renumber residues (RENUMBER)" \ help chain \ widget EDIT_MODE \ message "Old chain id (RENAME/RENUMBER)" \ widget RENUMBER_CHAIN -width 4 \ label "to" \ message "New chain id (RENAME/RENUMBER)" \ widget RENUMBER_NEW_CHAIN -width 4 \ label "for (optional) residue range" \ message "Optionally limit change of chain name to range (RENUMBER)" \ widget RENUMBER_RANGE_1 -width 6 \ label to \ widget RENUMBER_RANGE_2 -width 6 CloseSubFrame OpenSubFrame frame -toggle_display EDIT_MODE,$counter open RENUMBER CreateLineTemplate pdbset_renumber_form \ [list 0.0 0.25 0.35 0.45 0.5 0.65 0.8 ] CreateLineTemplate pdbset_renumber_form2 \ [list 0.0 0.25 0.35 0.5 0.65 0.8 ] CreateLine line \ message "Rename chain id and/or renumber residues (RENUMBER)" \ help renumber \ widget EDIT_MODE \ label "initial: " \ message "First residue in edit range (RENUMBER range)" \ widget RENUMBER_RANGE_1 -width 6 \ label "to" \ message "Last residue in edit range (RENUMBER range)" \ widget RENUMBER_RANGE_2 -width 6 \ message "Chain id of residues in edit range (RENUMBER CHAIN)" \ label "on chain" \ widget RENUMBER_CHAIN -width 4 \ format template pdbset_renumber_form CreateLine line \ help chain \ label "" \ label "result: " \ message "Rename chain id and/or renumber residues (RENUMBER)" \ widget RENUMBER_MODE \ widget RENUMBER_INIT \ label "Rename chain" \ message "New chain name (no change if blank) (RENUMBER new_chain)" \ widget RENUMBER_NEW_CHAIN -width 4 \ format template pdbset_renumber_form2 \ toggle_display RENUMBER_MODE,$counter open [list INIT ] CreateLine line \ help chain \ label "" \ message "Rename chain id and/or renumber residues (RENUMBER)" \ label "result: " \ widget RENUMBER_MODE \ widget RENUMBER_INC \ label "rename chain" \ message "New chain name (no change if blank) (RENUMBER new_chain)" \ widget RENUMBER_NEW_CHAIN -width 4 \ format template pdbset_renumber_form2 \ toggle_display RENUMBER_MODE,$counter open [list INC ] CloseSubFrame } #---------------------------------------------------------------- proc pdbset_replace { arrayname counter } { #---------------------------------------------------------------- OpenSubFrame frame \ -toggle_display REPLACE_MODE,$counter open REPLACE_RESIDUE CreateLine line \ help replace \ label "Rename " \ message "rename residue or atom type" \ widget REPLACE_MODE \ label "type" \ message "replace this residue type name" \ widget REPLACE_RES -width 4 \ label " as " \ message "by this residue type name" \ widget WITH_RES -width 4 CloseSubFrame OpenSubFrame frame \ -toggle_display REPLACE_MODE,$counter open REPLACE_ATOM CreateLine line \ help replace \ label "Rename " \ message "Rename residue or atom type" \ widget REPLACE_MODE \ label " type" \ message "replace this atom type name " \ widget REPLACE_ATOM -width 5 \ label " as " \ message "by this atom type name" \ widget WITH_ATOM -width 5 \ label " ( in residue " \ message "in this residue type" \ widget IN_RES -width 4 \ label " )" CloseSubFrame } #---------------------------------------------------------------- proc pdbset_symgen { arrayname counter} { #---------------------------------------------------------------- OpenSubFrame frame CreateLine line \ help symgen \ label "Symmetry operation to generate new chain: " \ label "$counter." \ message "Symmetry operation or NCS, eg X+1/2, Y+1/2, -Z" \ widget SYMGEN -width 20 CloseSubFrame OpenSubFrame frame \ -toggle_display SYMGEN,$counter open NCS hide CreateLineTemplate pdbset_ncs_matrix \ [ list 0.0 0.05 0.15 0.25 0.35 0.5 0.63 ] CreateLine line \ help transform \ label " " \ message "Fractional or orthogonal angstrom" \ label "Coordinate type: "\ widget NCS_ISFRACT \ label " " \ widget NCS_INVERT \ label "Invert transformation" CreateLine line \ label "" \ message "set elements of rotation" \ label "Rotation: " \ widget RN_11 \ widget RN_12 \ widget RN_13 \ message "set elements of translation" \ label "Translation: " \ widget TN_X \ format template pdbset_ncs_matrix CreateLine line \ label "" \ message "set elements of rotation" \ label "" \ widget RN_21 \ widget RN_22 \ widget RN_23 \ message "set elements of translation" \ label "" \ widget TN_Y \ format template pdbset_ncs_matrix CreateLine line \ label "" \ message "set elements of rotation" \ label "" \ widget RN_31 \ widget RN_32 \ widget RN_33 \ message "set elements of translation" \ label "" \ widget TN_Z \ format template pdbset_ncs_matrix CloseSubFrame } #---------------------------------------------------------------- proc pdbset_chain_rename { arrayname counter } { #---------------------------------------------------------------- OpenSubFrame frame CreateLine line \ help chain \ message "Rename chain after symmetry operation" \ label "Rename chain " \ message "original chain name" \ widget NSYM_OLD_CHAIN \ label " as " \ message "name after symmetry operation" \ widget NSYM_NEW_CHAIN \ label " generated by " \ message "which symmetry operation" \ widget NSYM_CHAIN_SYM \ label " symmetry operation" CloseSubFrame } #---------------------------------------------------------------- proc pdbset_output_atoms { arrayname counter } { #---------------------------------------------------------------- CreateLineTemplate pdbset_output_form \ [ list 0.0 0.15 0.25 0.35 0.45 0.55 ] OpenSubFrame frame if {$counter == 1 } { CreateLine line \ help pick \ label "Atom types" \ widget OUT_ATOM1 -width 4 \ widget OUT_ATOM2 -width 4 \ widget OUT_ATOM3 -width 4 \ widget OUT_ATOM4 -width 4 \ widget OUT_ATOM5 -width 4 \ format template pdbset_output_form } elseif {$counter > 1 && $counter <= 4 } { CreateLine line \ help pick \ label "" \ widget OUT_ATOM1 -width 4 \ widget OUT_ATOM2 -width 4 \ widget OUT_ATOM3 -width 4 \ widget OUT_ATOM4 -width 4 \ widget OUT_ATOM5 -width 4 \ format template pdbset_output_form } else { CreateLine line \ label "Maximum of 20" } CloseSubFrame } #---------------------------------------------------------------- proc pdbset_output_chains { arrayname counter } { #---------------------------------------------------------------- CreateLineTemplate pdbset_output_form \ [ list 0.0 0.15 0.25 0.35 0.45 0.55 ] OpenSubFrame frame if {$counter == 1 } { CreateLine line \ help select \ label "Chains" \ widget OUT_CHAIN1 -width 4 \ widget OUT_CHAIN2 -width 4 \ widget OUT_CHAIN3 -width 4 \ widget OUT_CHAIN4 -width 4 \ widget OUT_CHAIN5 -width 4 \ format template pdbset_output_form } elseif {$counter > 1 && $counter <= 4 } { CreateLine line \ help select \ label "" \ widget OUT_CHAIN1 -width 4 \ widget OUT_CHAIN2 -width 4 \ widget OUT_CHAIN3 -width 4 \ widget OUT_CHAIN4 -width 4 \ widget OUT_CHAIN5 -width 4 \ format template pdbset_output_form } else { CreateLine line \ label "Maximum of 20" } CloseSubFrame } #----------------------------------------------------------------- proc pdbset_update_task_action { arrayname } { #----------------------------------------------------------------- upvar #0 $arrayname array if { [GetValue $arrayname TASK_PRG] == "PDBCUR" } { set array(TASK_ACTION) $array(PDBCUR_ACTION) } else { set array(TASK_ACTION) $array(PDBSET_ACTION) } } #---------------------------------------------------------------- proc pdbset_task_window { arrayname } { #---------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Edit PDB File" "Edit PDB" \ [ list "Cell Parameters" \ "Rename chains and/or renumber residues" \ "Generate new chains by symmetry operations " \ "Rotations and translations" \ "Rename chains after symmetry operations" \ "Select elements for output" \ "Exclude elements for output" \ "Replace atom and residue types in pdb file" \ "Remove atoms with low/zero occupancy" ] ] == 0 } return SetProgramHelpFile "pdbset" # Special trap for backwards-compatibility # If you are re-running an old pdbset job, from before the # addition of pdbcur, we need to set new parameters correctly. # Non-zero XYZIN => re-running a job # Zero TASK_ACTION => re-running the old interface (or new job) if {$array(XYZIN) != "" && $array(TASK_ACTION) == ""} { set array(TASK_PRG) "PDBSET" } # Set TASK_ACTION from PDBSET_ACTION/PDBCUR_ACTION pdbset_update_task_action $arrayname #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Select operation to perform on PDB file (exclusive in template)" \ label "Use " \ widget TASK_PRG \ -command "pdbset_update_task_action $arrayname" \ label " to " \ widget PDBCUR_ACTION \ -command "pdbset_update_task_action $arrayname" \ toggle_display TASK_PRG open [ list PDBCUR ] hide CreateLine line \ message "Select operation to perform on PDB file (exclusive in template)" \ label "Use " \ widget TASK_PRG \ -command "pdbset_update_task_action $arrayname" \ label " to " \ widget PDBSET_ACTION \ -command "pdbset_update_task_action $arrayname" \ toggle_display TASK_PRG open [ list PDBSET ] hide #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input coordinate file name (XYZIN)" \ "PDB in" \ XYZIN DIR_XYZIN \ -fileout XYZOUT DIR_XYZOUT "_pdbset" \ -setfileparam space_group_name SPACE_GROUP \ -setfileparam space_group_name SYMGEN_GRP \ -setfileparam cell CELL CreateLine line \ message "Is input file from X-PLOR (XPLOR)" \ help xplor \ widget IFXPLOR \ label "" \ label "Input file is X-PLOR format" \ toggle_display TASK_PRG open [ list PDBSET ] hide CreateOutputFileLine line \ "Output coordinate file" \ "PDB out" \ XYZOUT DIR_XYZOUT CreateLine line \ message "Output to be in X-PLOR format" \ help output \ widget IFOUT_XPLOR \ label "" \ label "Output file X-PLOR format" \ toggle_display TASK_PRG open [ list PDBSET ] hide #=PARAMETERS========================================================== OpenFolder 1 TASK_PRG closed [ list PDBSET ] hide CreateLine line \ message "Space group (default from PDB) (SYMM)" \ help cell \ widget IF_CELL \ label "Reset cell parameters:" \ help spacegroup \ label " Space group" \ widget SPACE_GROUP CreateLine line \ message "Cell dimensions (default from PDB) (CELL)" \ help cell \ label "Cell a" \ widget CELL_1 \ label "b" \ widget CELL_2 \ label "c" \ widget CELL_3 \ label "alpha" \ widget CELL_4 \ label "beta" \ widget CELL_5 \ label "gamma" \ widget CELL_6 CreateLine line \ widget FROM_MTZ \ label "Use cell and space group parameters from MTZ file.." -italic \ toggle_display IF_CELL open 1 hide OpenSubFrame frame \ -toggle_display FROM_MTZ open 1 hide CreateInputFileLine line \ "Extract cell and space group parameters from MTZ file" \ "MTZ in" \ HKLIN DIR_HKLIN \ -setfileparam space_group_name SPACE_GROUP \ -setfileparam cell CELL CloseSubFrame CreateLine line \ help orthogonalization \ message "Define code to generate orthogonalization matrix" \ label "Define orthogonalization code: " \ widget PDBSET_NCODE \ toggle_display IF_CELL open 1 #=PARAMETERS2========================================================= OpenFolder 2 TASK_ACTION open [list RENAME ] hide CreateExtendingFrame NRENUMBER pdbset_renumber \ "Renumber residues or rename chain for a range of residues" \ "Add range of residues" \ [list EDIT_MODE \ RENUMBER_MODE \ RENUMBER_INIT \ RENUMBER_RANGE_1 \ RENUMBER_RANGE_2 \ RENUMBER_CHAIN \ RENUMBER_NEW_CHAIN ] #=PARAMETERS3========================================================= OpenFolder 3 TASK_ACTION open [list SYMMETRY ] hide CreateLine line \ help symgen \ message "Select method for entering symmetry operations" \ label "Use" \ widget SYMGEN_MODE \ label "to define symmetry operations" CreateLine line \ help symgen \ message "Enter spacegroup name or number (SPACEGROUP)" \ label "Spacegroup:" \ widget SYMGEN_GRP \ toggle_display SYMGEN_MODE open [ list SYMGEN_SPACE ] OpenSubFrame frame \ -toggle_display SYMGEN_MODE open SYMGEN_OP hide CreateLine line \ label "List of individual symmetry operators:" CreateExtendingFrame NSYMGEN pdbset_symgen \ "Symmetry operations to generate new chains" \ "Add new symmetry operation to list"\ [list SYMGEN RN_11 RN_21 RN_31 RN_12 RN_22 RN_32 RN_13 \ RN_23 RN_33 TN_X TN_Y TN_Z NCS_ISFRACT NCS_INVERT ] CloseSubFrame #=PARAMETERS4========================================================= OpenFolder 4 TASK_ACTION open [list ROTATE ] hide CreateLine line \ message "coordinate shift to be performed" \ label "Apply " \ widget TRANS_TYPE \ label "to coordinates." \ label " " \ message "Require inverse of translation" \ widget NCS_TRAN_INVERT \ label "Invert transformation" CreateLine line \ help rotate \ message "Matrix, Polar angles, Euler angles" \ label "Define rotation in terms of: " \ widget NCS_ROT_TYPE \ toggle_display TRANS_TYPE open [list ROTATE BOTH ] CreateLine line \ help rotate \ message "Coordinate system, orthogonal angstrom or fractional" \ label "Coordinate system: " \ widget NCS_TRAN_ISFRACT \ toggle_display TRANS_TYPE open [list SHIFT BOTH ] CreateLineTemplate pdbset_ncs_matrix \ [ list 0.0 0.15 0.25 0.35 ] OpenSubFrame frame \ -toggle_display TRANS_TYPE open [list ROTATE BOTH ] hide OpenSubFrame frame \ -toggle_display NCS_ROT_TYPE open [list MATRIX ] hide CreateLine line \ help rotate \ message "set elements of rotation" \ label "Rotation: " \ widget R_11 \ widget R_12 \ widget R_13 \ format template pdbset_ncs_matrix CreateLine line \ help rotate \ message "set elements of rotation" \ label "" \ widget R_21 \ widget R_22 \ widget R_23 \ format template pdbset_ncs_matrix CreateLine line \ help rotate \ message "set elements of rotation" \ label "" \ widget R_31 \ widget R_32 \ widget R_33 \ format template pdbset_ncs_matrix CloseSubFrame OpenSubFrame frame \ -toggle_display NCS_ROT_TYPE open [list EULER] hide CreateLine line \ help rotate \ message "set elements of rotation" \ label "Eulerian angles: " \ label "Alpha Beta Gamma" \ widget R_ALPHA \ widget R_BETA \ widget R_GAMMA \ format template pdbset_ncs_matrix CloseSubFrame OpenSubFrame frame \ -toggle_display NCS_ROT_TYPE open [list POLAR] hide CreateLine line \ help rotate \ message "set elements of rotation" \ label "Polar angles: " \ label "Omega Phi Kappa" \ widget R_OMEGA \ widget R_PHI \ widget R_KAPPA \ format template pdbset_ncs_matrix CloseSubFrame CloseSubFrame OpenSubFrame frame \ -toggle_display TRANS_TYPE open [list SHIFT BOTH ] hide CreateLine line \ help shift \ message "set elements of translation" \ label "Translation: " \ label "x-axis y-axis z-axis" \ widget T_X \ widget T_Y \ widget T_Z \ format template pdbset_ncs_matrix CloseSubFrame #=PARAMETERS5========================================================= OpenFolder 5 TASK_ACTION open [list SYMMETRY ] hide CreateExtendingFrame NSYM_CHAIN_RENAME pdbset_chain_rename \ "Rename symmetry operation generated chains" \ "Add to list of renamed chains" \ [list NSYM_CHAIN_SYM NSYM_OLD_CHAIN NSYM_NEW_CHAIN ] #=PARAMETERS6========================================================= OpenFolder 6 TASK_ACTION open [list SELECT ] hide CreateLine line \ help pick \ message "Select specified atom types" \ widget OUTPUT_PICK \ label "" \ label "Select by atom type for inclusion in pdb file." OpenSubFrame frame \ -toggle_display OUTPUT_PICK open 1 hide CreateExtendingFrame NOUT_ATOMS pdbset_output_atoms \ "Select atom type(s), case sensitive" \ "Add further atom types (max. 20)" \ [list OUT_ATOM1 OUT_ATOM2 OUT_ATOM3 OUT_ATOM4 \ OUT_ATOM5 ] CloseSubFrame CreateLine line \ help select \ message "Select only specified chains" \ widget OUTPUT_CHAIN \ label "" \ label "Select by chain name." OpenSubFrame frame \ -toggle_display OUTPUT_CHAIN open 1 hide CreateExtendingFrame NOUT_CHAINS pdbset_output_chains \ "Select chain(s), case sensitive" \ "Add further chains (max. 20)" \ [list OUT_CHAIN1 OUT_CHAIN2 OUT_CHAIN3 OUT_CHAIN4 \ OUT_CHAIN5 ] CloseSubFrame CreateLine line \ help select \ message "Selection based on occupancy" \ widget OUTPUT_OCCUPANCY \ label "" \ label "Select only atoms with occupancy greater than minimum." CreateLine line \ message "Select atoms with occupancy greater than value" \ label "Occupancy greater than" \ widget OUTPUT_SEL_OCC -width 6 \ toggle_display OUTPUT_OCCUPANCY open 1 CreateLine line \ help select \ message "Selection based on B-factor" \ widget OUTPUT_BFACTOR \ label "" \ label "Select only atoms with B-factor less than maximum." CreateLine line \ message "Select atoms with B less than value" \ label "B-factor less than" \ widget OUTPUT_SEL_BFACT -width 6 \ toggle_display OUTPUT_BFACTOR open 1 #=PARAMETERS7========================================================= OpenFolder 7 TASK_ACTION open [list SELECT ] hide CreateLine line \ help exclude \ message "Exclude header information, useful for merging pdb files" \ widget EXCLUDE_HEADER \ label "" \ label "Exclude header information from pdb file." \ message "Exclude side chains, beyond CB" CreateLine line \ help exclude \ message "Exclude side chains from pdb file." \ widget EXCLUDE_SIDE \ label "" \ label "Exclude side chains." CreateLine line \ help exclude \ message "Exclude water groups from pdb file" \ widget EXCLUDE_WATER \ label "" \ label "Exclude water molecules." #=PARAMETERS8========================================================= OpenFolder 8 TASK_ACTION open [list REPLACE ] hide CreateExtendingFrame NREPLACE pdbset_replace \ "Replace residues or atoms" "Add to list of replacements" \ [list REPLACE_MODE REPLACE_RES WITH_RES \ IN_RES REPLACE_ATOM WITH_ATOM] SetProgramHelpFile "pdbcur" #=CUTOCC PARAMETERS9================================================= OpenFolder 9 TASK_ACTION open [list CUTOCC ] hide CreateLine line \ help cutocc \ message "Delete all atoms with an occupancy less than or equal to cutoff." \ label "Delete all atoms with an occupancy less than or equal to " \ widget CUTOCC_CUTOFF }