CHARMM Element doc/intcor.doc 1.1#File: INTCOR, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax The Internal Coordinate Manipulation Commands The commands in this section can be used to construct cartesiancoordinates from internal coordinate values. The internal coordinatedata structure can also be used for analysis purposes.There are flexible editing commands for manipulating the data structure.When these commands are used in conjunction with the CoordinateManipulation commands (see *note Corman:(chmdoc/corman.doc).) and theI/O commands (see *note IO:(chmdoc/io.doc).), a rather complete modelbuilding facility exists.* Menu:* Syntax:: Syntax of the internal coordinate commands* Function:: Purpose of each of the commands* Structure:: Description of the structure of internal coordinates#File: INTCOR, Node: Syntax, Up: Top, Next: Function, Previous: Top Syntax of Internal Coordinates commands[SYNTAX IC - internal coordinate tables] IC { PARAmeters [ALL] } { FILL [COMP] [APPEnd] [PREServe] [SAVEd] } { GENErate [THREe] atom-selection } { DIFFerences [COMP] [APPEnd] [SCALe real] } { DERIvatives [COMP] [APPEnd] [DELTa real] } { DYNAmics dynamics-spec } { EDIT } { BUILd [COMP] [SAVEd] } { SEED atom atom atom [COMP] } { PURGe [SAVEd] } { ADD [SAVEd] } { SUBTract [SAVEd] } { SCALe scale-spec [SAVEd] } { RANDom [ISEEd int] [SAVEd] } { GAUSsian UNIT int atom atom atom } { PUCKer 5x(atom) ANGLe real AMPL real } { } { { DELete } { BYNUM int [int] } [SAVEd] } { { KEEP } { ic-selection } } { } { SAVE [PREServe ] } { RESTore [OVERwrite] } { } { READ [FILE] [APPEnd] UNIT int [SAVEd] } { } { WRITe [FILE] [RESId] UNIT int [SAVEd] } { } { PRINt [SAVEd] }atom::= { residue-number atom-name } { segid resid atom-name } { BYNUm atom-number } { next-from-atom-selection }dynamics-spec::= { [AVERages] } [FIRStunit int] [NUNIts int] { FLUCtuations } [BEGIn int] [STOP int] [NSKIp int]ic-selection::= { } atom-selection { [FIRSt] [SECOnd] [THIRd] [FOURth] [IMPR] } { [DIHE] }scale-spec ::= [ BOND real ] [ ANGLe real ] [ DIHEdral real ]atom-selection ::= see *note select:(chmdoc/select.doc).next-from-atom-selection ::= all atoms are selected from a single atom selection in sequential order. The syntax for the EDIT subcommands are:{ DISTance atom atom real [ADD] }{ ANGLe atom atom atom real [ADD] }{ DIHEdral { atom atom [*]atom atom } real [ADD] }{ { ICNUmber integer } }{ END }#File: INTCOR, Node: Function, Up: Top, Next: Structure, Previous: Syntax Purpose of the various Internal Coordinate commandsDescription : These commands are used to setup, modify and process theinternal coordinates of the molecule. This operation is very usefulin setting up atom coordinates whenever they are not known. Thisoccurs when a protein structure is built from scratch or when anexisting structure is modified. The modification can be simply aconformational change, or a change in the residue sequence throughreplacement, insertion, or deletion. Many of these modifications canbe processed within the program as it currently stands. Other moredifficult modifications can be facilitated by editing the internalcoordinate card file by using external programs. This facility is also useful as an analysis tool. Several supportprogram use the output from IC tables for conformational analysis(phi-psi maps, ring pucker, pseudorotational angles, solvent structure,...).Command ordering : The Internal Coordinate commands (except EDIT and READ) can only beused if internal coordinates exist (i.e. if the IC common is filled).This can only be filled by reading an IC file, or by using the SETUpkeyword in the GENErate or PATCh commands. The information used to setupis obtained from the residue topology file used in the generation process.Subcommand interpretation :------------------------------------------------------------------------------PARAmeter [ALL] - Fill table with parameter values Fill the internal coordinates using standard values fromthe parameter file, unless otherwise specified in the residue topologyfile (see RTF:(IO)Rtf File Formats.). A value of zero for any bond orangle (not dihedral) indicates that this value should be obtainedfrom the parameters. If the ALL keyword is specified, then all angleand bond values will be filled from the parameter set regardless of theexisting values. Setting bond and angles values to zero with the IC editcommand makes it possible to selectively use this command.------------------------------------------------------------------------------FILL [COMP] [APPEnd] [PREServe] - Convert from cartesian to internal coordinatesFill the internal coordinate values wherever possible from theknown atomic coordinates. IC's for atoms that are not placed are zeroedunless the PREServe keyword is specified, in which case the entries are notmodified. If the COMP keyword is used, then The alternate coordinate setwill be used to fill the IC data structure. The APPEnd option will addthe current values to the existing values of the table.For example, one way to see how the current coordinates match a referenceic table: ic scale bond -1.0 angle -1.0 dihe -1.0 ic fill