{+ file: get_ncs_matrices.inp +} {+ directory: general +} {+ description: Determine NCS operators between molecules +} {+ comment: Uses the current coordinates to determine the NCS operators between molecules. +} {+ authors: Axel T. Brunger, and Paul D. Adams +} {+ copyright: Yale University +} {- Guidelines for using this file: - all strings must be quoted by double-quotes - logical variables (true/false) are not quoted - do not remove any evaluate statements from the file -} {- begin block parameter definition -} define( {============================ coordinates ============================} {* coordinate file *} {===>} coordinate_infile="eg1_dimer.pdb"; {==================== molecular information ==========================} {* topology files *} {===>} topology_infile_1="CNS_TOPPAR:protein.top"; {===>} topology_infile_2="CNS_TOPPAR:dna-rna.top"; {===>} topology_infile_3="CNS_TOPPAR:water.top"; {===>} topology_infile_4="CNS_TOPPAR:ion.top"; {===>} topology_infile_5="CNS_TOPPAR:carbohydrate.top"; {===>} topology_infile_6=""; {===>} topology_infile_7=""; {===>} topology_infile_8=""; {* linkage files for linear, continuous polymers (protein, DNA, RNA) *} {===>} link_infile_1="CNS_TOPPAR:protein.link"; {===>} link_infile_2="CNS_TOPPAR:dna-rna-pho.link"; {===>} link_infile_3=""; {* parameter files *} {===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param"; {===>} parameter_infile_2="CNS_TOPPAR:dna-rna_rep.param"; {===>} parameter_infile_3="CNS_TOPPAR:water_rep.param"; {===>} parameter_infile_4="CNS_TOPPAR:ion.param"; {===>} parameter_infile_5="CNS_TOPPAR:carbohydrate.param"; {===>} parameter_infile_6=""; {===>} parameter_infile_7=""; {===>} parameter_infile_8=""; {* molecular topology file: optional (leave blank for auto generation) *} {* Auto generation of the molecular topology from the coordinates should only be used if: (1) Each distinct protein, DNA, or RNA chain must have a separate segid (or chainid if the chainid is non-blank). (2) Each contiguous protein, RNA, or RNA chain must not be disrupted by other types of residues or ligands. Rather, these other residues should be listed after protein, RNA/DNA chains. (3) Disulphides are automatically detected based on distances between the sulfur atoms (must be less than 3 A apart). (4) Broken protein/RNA/DNA chains without terminii must be more than 2.5 A apart to be recognized as such. (5) N-linked glycan links are automatically recognized if the bonded atoms are less than 2.5 A apart. (6) Automatic generation cannot be used with alternate conformations. For ligands, the user must make suitable topology and parameter files. For non-standard covalent linkages, the custom patch file should be used. Alternatively, the generate.inp or generate_easy.inp task files can be used to generated the mtf prior to running this task file. *} {===>} structure_infile="eg1_dimer.mtf"; {* for auto generation: extra linkages and modifications by custom patches *} {===>} patch_infile=""; {========================== atom selection ===========================} {* select atoms in primary (reference) molecule *} {===>} atom_ref=(segid AAAA and name CA); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_1=(segid CCCC and name CA); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_2=(none); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_3=(none); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_4=(none); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_5=(none); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_6=(none); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_7=(none); {* select atoms in NCS related molecule (use none if not used) *} {===>} atom_ncs_8=(none); {* ignore atom names when comparing NCS related atoms *} {+ choice: true false +} {===>} ignore_name=false; {=========================== output files ============================} {* output listing file with NCS operators *} {===>} list_outfile="get_ncs_matrices.list"; {===========================================================================} { things below this line do not normally need to be changed } {===========================================================================} ) {- end block parameter definition -} checkversion 1.3 evaluate ($log_level=quiet) if ( $log_level = verbose ) then set message=normal echo=on end else set message=off echo=off end end if if ( &BLANK%structure_infile = true ) then {- read topology files -} topology evaluate ($counter=1) evaluate ($done=false) while ( $done = false ) loop read if ( &exist_topology_infile_$counter = true ) then if ( &BLANK%topology_infile_$counter = false ) then @@&topology_infile_$counter end if else evaluate ($done=true) end if evaluate ($counter=$counter+1) end loop read end @CNS_XTALMODULE:mtfautogenerate ( coordinate_infile=&coordinate_infile; convert=true; separate=true; atom_delete=(not known); hydrogen_flag=true; break_cutoff=2.5; disulphide_dist=3.0; carbo_dist=2.5; patch_infile=&patch_infile; O5_becomes="O"; ) else structure @&structure_infile end coordinates @&coordinate_infile end if {- read parameter files -} parameter evaluate ($counter=1) evaluate ($done=false) while ( $done = false ) loop read if ( &exist_parameter_infile_$counter = true ) then if ( &BLANK%parameter_infile_$counter = false ) then @@¶meter_infile_$counter end if else evaluate ($done=true) end if evaluate ($counter=$counter+1) end loop read end set message=normal echo=on end if ( &ignore_name = true ) then do (name="CA") (all) end if set display=&list_outfile end display >>>> NCS operators for: display >>>> coordinate file= &STRIP%coordinate_infile display display ====================================================================== display evaluate ($done=false) evaluate ($counter=1) while ( $done = false ) loop group if ( &exist_atom_ncs_$counter = true ) then show sum(1) (&atom_ncs_$counter) if ( $result > 0 ) then ncs restraints init group equiv=&atom_ref equiv=&atom_ncs_$counter end ? end display NCS operator which transforms: display &atom_ref -> &atom_ncs_$counter display display matrix= ( $rot_1_2_1_1[f8.5] $rot_1_2_1_2[f8.5] $rot_1_2_1_3[f8.5] ) display ( $rot_1_2_2_1[f8.5] $rot_1_2_2_2[f8.5] $rot_1_2_2_3[f8.5] ) display ( $rot_1_2_3_1[f8.5] $rot_1_2_3_2[f8.5] $rot_1_2_3_3[f8.5] ) display translation= ( $rot_1_2_1_4[f10.5] $rot_1_2_2_4[f10.5] $rot_1_2_3_4[f10.5] ) display display rms difference= $rot_1_2_rmsd[f8.5] display display ====================================================================== display end if evaluate ($counter=$counter+1) else evaluate ($done=true) end if end loop group display Inverse operators display display ====================================================================== display evaluate ($done=false) evaluate ($counter=1) while ( $done = false ) loop group if ( &exist_atom_ncs_$counter = true ) then show sum(1) (&atom_ncs_$counter) if ( $result > 0 ) then ncs restraints init group equiv=&atom_ref equiv=&atom_ncs_$counter end ? end display Inverse NCS operator which transforms: display &atom_ncs_$counter -> &atom_ref display display matrix= ( $rotinv_1_2_1_1[f8.5] $rotinv_1_2_1_2[f8.5] $rotinv_1_2_1_3[f8.5] ) display ( $rotinv_1_2_2_1[f8.5] $rotinv_1_2_2_2[f8.5] $rotinv_1_2_2_3[f8.5] ) display ( $rotinv_1_2_3_1[f8.5] $rotinv_1_2_3_2[f8.5] $rotinv_1_2_3_3[f8.5] ) display translation= ( $rotinv_1_2_1_4[f10.5] $rotinv_1_2_2_4[f10.5] $rotinv_1_2_3_4[f10.5] ) display display rms difference= $rotinv_1_2_rmsd[f8.5] display display ====================================================================== display end if evaluate ($counter=$counter+1) else evaluate ($done=true) end if end loop group stop