# ======================================================================= # phaser_NMA.tcl -- # # Phaser Model Generation (NMA) # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------------ proc phaser_NMA_prereq { } { #------------------------------------------------------------------------------ if { ![file exists [FindExecutable phaser]] } { return 0 } return 1 } #------------------------------------------------------------------------ proc phaser_NMA_setup { typedefVar arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefVar typedef upvar #0 $arrayname array DefineMenu _mode_menu [list "SCEDS domain division" \ "Perturb coordinates" ] \ [list "DOMAIN" \ "PERTURB" ] DefineMenu _eigen_type \ [list "Write to file" "Do not write to file" "Read from file"] \ [list "WRITEON" "WRITEOFF" "READ"] DefineMenu _perturb_type \ [list " RMS " " DQ " ] [list "RMS" "DQ"] DefineMenu _method_type \ [list "rotation-translation blocks" "C-alpha atoms only" "All atoms" ] \ [list "RTB" "CA" "ALL" ] DefineMenu _perturb_dir \ [list "forward" "backward" "to-and-fro" ] [list "FORWARD" "BACKWARD" "TOFRO"] set typedef(_onoff) \ { menu { "on" "off" } { ON OFF } } DefineMenu _rmsid_option \ [list "rms difference" "sequence identity" ] [list "RMS" "IDENT" ] set typedef(_mat_file) { file MATRIX ".mat" "Phaser matrix file" { "Text Browser" } { DisplayTextFile } } return 1 } #------------------------------------------------------------------------ proc phaser_NMA_run { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(OUTPUT_FILES) "" if { $array(NMA_XYZIN) == "" } { WarningMessage "NOT SET: pdb file" return 0 } if { $array(ENSEMBLE_ID_NMA) == "" } { WarningMessage "NOT SET: ensemble name for SOL file output" return 0 } if { $array(RMS_NMA) == "" } { WarningMessage "NOT SET: sequence identity or RMS deviation for SOL file output" return 0 } if { ([GetValue $arrayname NMA_EIGEN] == "READ") && $array(EIGENIN) == "" } { WarningMessage "NOT SET: eigen file" return 0 } if { $array(N_NMA_MODES) == 0 } { WarningMessage "NOT SET: modes for perturbation" return 0 } for { set n 1 } { $n <= $array(N_NMA_MODES) } { incr n } { if { $array(NMA_MODE,$n) == "" } { WarningMessage "NOT SET: normal mode perturbation value" return 0 } } if { ([GetValue $arrayname NMA_METHOD] == "RTB") } { if { $array(TOG_NMA_MAXB) && $array(NMA_MAXB) == "" } { WarningMessage "NOT SET: Maximum number of blocks" return 0 } if { $array(TOG_NMA_NRES) && $array(NMA_NRES) == "" } { WarningMessage "NOT SET: Number of residues per block" return 0 } } if { ([GetValue $arrayname NMA_PERTURB] == "DQ") } { if { $array(N_NMA_DQ) == 0 } { WarningMessage "NOT SET: DQ steps" return 0 } } if { ([GetValue $arrayname NMA_PERTURB] == "DQ") } { for { set n 1 } { $n <= $array(N_NMA_DQ) } { incr n } { if { $array(NMA_DQ,$n) == "" } { WarningMessage "NOT SET: normal mode dq" return 0 } } } if {([GetValue $arrayname NMA_PERTURB] == "RMS")} { if { $array(NMA_RMSINC) == "" } { WarningMessage "NOT SET: RMS step" return 0 } if { $array(NMA_MAXRMS) == "" } { WarningMessage "NOT SET: Max RMS distance" return 0 } if { $array(TOG_NMA_CLASH) && $array(TOG_NMA_CLASH) == "" } { WarningMessage "NOT SET: Clash distance between atoms" return 0 } if { $array(TOG_NMA_STRETCH) && $array(TOG_NMA_STRETCH) == "" } { WarningMessage "NOT SET: Stretch distance between atoms" return 0 } } if { $array(TOG_NMA_FORCE) && $array(NMA_FORCE) == "" } { WarningMessage "NOT SET: Elastic Network Model force constant" return 0 } if { $array(TOG_NMA_RADIUS) && $array(NMA_RADIUS) == "" } { WarningMessage "NOT SET: Elastic Network Model interaction radius" return 0 } if { $array(TOG_NMA_COMBINATION) && $array(NMA_NCOMB) == "" } { WarningMessage "NOT SET: Number of modes to combine at a time" return 0 } set array(INPUT_FILES) "NMA_XYZIN" if { ([GetValue $arrayname NMA_EIGEN] == "READ") } { append array(INPUT_FILES) " EIGENIN" } return 1 } #------------------------------------------------------------------------ proc phaser_NMA_dq_list { arrayname counter_dqs } { #------------------------------------------------------------------------ # The auto search extending frame code for adding dqs upvar #0 $arrayname array CreateLine line \ label " " \ label "Perturb with DQ " widget NMA_DQ -oblig } #------------------------------------------------------------------------ proc phaser_NMA_mode_list { arrayname counter_modes } { #------------------------------------------------------------------------ # The auto search extending frame code for adding modes upvar #0 $arrayname array CreateLine line \ label "Perturb along mode " widget NMA_MODE -oblig } #------------------------------------------------------------------------ proc phaser_NMA_task_window {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array # global configure if { [CreateTaskWindow $arrayname \ "Normal Mode Analysis"\ "Phaser" \ [ list "Define data" \ "Define modes" \ "Define SCEDS parameters" \ "Define perturbations" \ "Output control" \ "Expert DDM parameters" \ "Expert ENM parameters" ] ] == 0 } return # SetProgramHelpFile phaser #=PROTOCOL=============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ label "Mode for normal mode analysis" \ message "Select the aim of the NMA" \ widget NMA_DOMAIN CreateLine line \ message "Number of processors (parallelization)" \ widget TOG_NJOBS -toggleon \ label "Number of processors "\ widget NJOBS \ label "(only relevant if phaser compiled with openmp option)" #=FILES================================================================== # The "Define data" folder for Normal Mode Analysis OpenFolder 1 open CreateInputFileLine line \ "Select a PDB file" \ "PDB file" \ NMA_XYZIN DIR_NMA_XYZIN #======================================================================== # The "Define modes" folder for Normal Mode Analysis OpenFolder 2 open CreateLine line \ label "Note: Mode 7 is the lowest non-trivial mode (after the 3 rotation and 3 translation modes)" -italic CreateLine line \ label "Note: Mode n < 7 is taken to mean the first n modes starting at mode 7 (e.g. 5=7,8,9,10,11)" -italic CreateExtendingFrame N_NMA_MODES phaser_NMA_mode_list \ "Perturb along mode" \ "Add a mode for perturbation" \ [list NMA_MODE] CreateLine line \ widget TOG_NMA_COMBINATION -toggleon \ label "Number of modes to combine at a time" \ widget NMA_NCOMB #======================================================================== # The "Define SCEDS parameters" folder for Normal Mode Analysis OpenFolder 3 NMA_DOMAIN hide [list PERTURB ] open CreateLine line \ message "Number of domains into which to split the protein" \ widget TOG_NMA_NUMB -toggleon label "Split PDB file into" widget NMA_NUMB label "domains" \ toggle_display NMA_DOMAIN open DOMAIN CreateLine line \ message "Use the Equality condition to score domains" \ widget TOG_NMA_WEIG -toggleon \ label "SCEDS Weights: Sphericity " widget NMA_WEIG_SPHE -width 5 \ label "Continutity " widget NMA_WEIG_CONT -width 5 \ label "Equality " widget NMA_WEIG_EQUA -width 5 \ label "Density " widget NMA_WEIG_DENS -width 5 \ toggle_display NMA_DOMAIN open DOMAIN #======================================================================== # The "Perturbation parameters" folder for Normal Mode Analysis OpenFolder 4 NMA_DOMAIN hide [list DOMAIN ] open CreateLine line \ label "Perturb structure in " widget NMA_PERTURB \ label "steps" CreateLine line \ label " " \ message "RMS deviation step size" \ label "RMS step" widget NMA_RMSINC \ label "Max RMS distance" widget NMA_MAXRMS \ label "Direction" widget NMA_DIRECTION \ toggle_display NMA_PERTURB open RMS CreateLine line \ label " " \ widget TOG_NMA_CLASH -toggleon \ label "Perturbation stops when any two atoms come within" widget NMA_CLASH \ label "Angstroms" \ toggle_display NMA_PERTURB open RMS CreateLine line \ label " " \ widget TOG_NMA_STRETCH -toggleon \ label "Perturbation stops when a bond stretches past" widget NMA_STRETCH \ label "Angstroms" \ toggle_display NMA_PERTURB open RMS OpenSubFrame frame -toggle_display NMA_PERTURB open [list DQ ] hide CreateExtendingFrame N_NMA_DQ phaser_NMA_dq_list \ "Perturb with dq" \ "List DQ steps explicitly" \ [list NMA_DQ] CloseSubFrame # #======================================================================== # The "Output control" folder for Normal Mode Analysis OpenFolder 5 closed CreateLine line \ message "Controls output of PDB files containing potential solutions.\ Default depends on mode." \ widget TOG_XYZOUT -toggleon \ label "PDB file output" \ widget XYZOUT_ONOFF CreateLine line \ message "For output sol file" \ label "Ensemble ID" -italic \ widget ENSEMBLE_ID_NMA CreateLine line \ message "For output sol file" \ label "Similarity of output PDB files to target structure" -italic \ widget ENSEMBLE_RMSID_OPTION_NMA \ widget RMS_NMA -oblig CreateLine line \ message "VERBOSE: more information included in log file than by default" \ widget TOG_VERBOSE \ label "Verbose output to log file" \ CreateLine line \ message "DEBUG: debugging information included in log file than by default" \ widget TOG_VERBOSE_EXTRA \ label "Debug output to log file" CreateLine line \ widget TOG_NMA_EIGEN -toggleon\ label "Eigenvalues and Eigenvectors" \ message "Read or Write Eigenvalues and Eigenvectors" \ widget NMA_EIGEN CreateInputFileLine line \ "Eigen File input MUST have been generated with an identical NMA Method" \ "Eigen File" \ EIGENIN DIR_EIGENIN \ -toggle_display NMA_EIGEN open READ hide #======================================================================== # The "Expert DDM parameters" folder for Normal Mode Analysis OpenFolder 6 NMA_DOMAIN hide [list PERTURB ] closed CreateLine line \ message "Control the parameters for domain assignments" \ widget TOG_NMA_DDM -toggleon \ label "DDM Distances: " \ label "Min " widget NMA_DDM_MIN \ label "Max " widget NMA_DDM_MAX \ label "Step " widget NMA_DDM_STEP CreateLine line \ message "Control the parameters for domain assignments" \ widget TOG_NMA_SLI -toggleon \ label "DDM Slider: " \ label "Slider " widget NMA_DDM_SLID CreateLine line \ message "Control the parameters for domain assignments" \ widget TOG_NMA_DIST -toggleon \ label "DDM through-space separation (Angstroms): " \ label "Min " widget NMA_DIST_MIN \ label "Max " widget NMA_DIST_MAX CreateLine line \ message "Control the parameters for domain assignments" \ widget TOG_NMA_SEQU -toggleon \ label "DDM sequence separation: " \ label "Min " widget NMA_SEQU_MIN \ label "Max " widget NMA_SEQU_MAX CreateLine line \ message "Control the parameters for domain assignments" \ "(negative: use length dependent defaults)" \ widget TOG_NMA_JOIN -toggleon \ label "Sequence Joining Length: " \ label "Min " widget NMA_JOIN_MIN \ label "Max " widget NMA_JOIN_MAX #======================================================================== # The "Expert ENM parameters" folder for Normal Mode Analysis OpenFolder 7 closed CreateLine line \ message "Controls NMA method" \ widget TOG_NMA_METHOD -toggleon \ label "Elastic Network Model" \ widget NMA_METHOD CreateLine line \ label " " \ widget TOG_NMA_NRES -toggleon \ label "Number of residues per block" \ widget NMA_NRES \ toggle_display NMA_METHOD open RTB hide CreateLine line \ label " " \ widget TOG_NMA_MAXB -toggleon \ label "Maximum number of blocks" \ widget NMA_MAXB \ toggle_display NMA_METHOD open RTB hide CreateLine line \ widget TOG_NMA_FORCE -toggleon \ label "Elastic Network Model force constant" widget NMA_FORCE CreateLine line \ widget TOG_NMA_RADIUS -toggleon \ label "Elastic Network Model interaction radius" widget NMA_RADIUS label "Angstroms" }