Include file: Mainly needed for: ANATRA.INC Trajectory analysis BIGINC.INC Everywhere CHESS.INC Chess playing module CMPINC.INC CNTINC.INC COMINC.INC CONFAC.INC ELMDAT.INC ELMINC.INC EPSINC.INC EQUFLD.INC Chess playing module ESPACE.INC Anywhere where 'dynamical memory allocation' is needed FDEVIC.INC GL graphics FGLINC.INC GL graphics FRACTI.INC Spline option GENINC.INC HB2INC.INC Hydrogen bonds HBONDS.INC Hydrogen bonds HGRINC.INC Hydrogen bonds INDCES.INC Spline option IRIGRA.INC Graphics MCXINC.INC Monte Carlo procedure MDFINC.INC H,K,L,F file inspection NEURON.INC Neural network PDBINC.INC PDB file verification PIRINC.INC Obsolete sequence menu QUALTY.INC Packing quality control REFINC.INC Structure regularization SELECT.INC Protein selection SPCIAL.INC Special options STKVLD.INC Chess playing module SUPPOS.INC Three dimensional superposition SYMANA.INC Symmetry SYMDAT.INC Symmetry SYMINC.INC Symmetry TABLES.INC Spead sheet WALIGN.INC New sequence manipulation menus
SYMSTAT_DELETED Matrix is flagged to be deleted SYMSTAT_FILEF = Matrix read from file in fractional coordinates SYMSTAT_FILEO = Matrix read from file in orthogonal coordinates SYMSTAT_MTRIX = Matrix read from mtrix cards on PDB file SYMSTAT_SPGRP = Matrix generated by space group symmetry routine SYMSTAT_SYMTR = Matrix read from symtr cards on PDB file SYMSTAT_TRANS = Matrix has been generated by translation SYMSTAT_USERF = Matrix entered by user in fractional coordinates SYMSTAT_USERO = Matrix entered by user in orthogonal coordinates HB2IDN remembers whether the initialization is done *COOR1 saves the coordinates of the native residues temporarily *COOR2 saves the coordinates of the rotated residues temporarily ACCES1 saves the accessibility in the native form ACCES2 saves the accessibility in the non-native form ARAD stores affected donors ARIATA stores (1 or 2) acceptor IATs for each H atom. ARIATD stores donor IATs ARPAAT stores potential acceptor IATs ARPAIS stores potential acceptor ISYMs ARSYMA stores (1 or 2) acceptor ISYMs for each H atom. ARVALA stores (1 or 2) H-bond values for each H atom. ARXYZH stores fixed and flexible H-atom coordinates. ATDON saves the donor number CURCUR stores the connections between members of the subnet CURR stores the IAMB numbers for each member of the subnet DONAMB stores the index in the "ambiguity" arrays EXVAL saves the exposure value HB2ACB saves the connected atom numbers for each acceptor HB2ACT saves the acceptor type 1-9 for all acceptors HB2AMB stores the number of possibilities HB2ANG stores the IANG within the residue HB2AUT stores the D-H.A look-up-table from HBOFIELD.DAT HB2BES stores the best scoring configuration so far HB2DLY number of degrees for lysine steps HB2DON stores the index in the array of donors for the ambiguity HB2DSE number of degrees for serine steps HB2DST stores the fixed residue HB2DUT stores the H...A look-up-table from HBOFIELD.DAT HB2DVA stores the summed-up hbond values HB2ERT is the same, expressed in RT units. HB2EXV is the expected value of a hydrogen bond to invisible water. HB2FAM stores the original ambiguity for the fixed residue HB2FIN stores the index in the HB2FFX array HB2FLP stores the total flip penalty HB2GRC stores the number of H atoms HB2GRP stores the group number HB2GRT stores the group type HB2H2N stores the nearest other conformations for each conformation HB2IAA stores the IAA in question HB2IAT stores the IAT within the residue (overlayed with HB2ANG!) HB2LUT stores the look-up-table acceptor geometry from HBOFIELD.DAT HB2LYS number of possibilities for lysine+the like HB2MXE is the maximum energy for a Hydrogen bond HB2ORG stores the original angle value from CHI004 HB2ORS stores the fixing residue HB2PEN stores the penalty for a residue not being in the "1" position HB2POS stores the position-# of the configuration under consideration HB2SER number of possibilities for serine+the like HB2TYP stores the donor type from HBOTYP (overlayed with HB2ORG!) HB2WHA stores the Wanted Hydrogen bond Acceptor HB2WHD stores the Wanted Hydrogen bond Donor INAD stores the index in the array of affected donors for the ambiguity. INDON stores an index in the list of donors INPA stores the index in the array of potential acceptors INTT stores the index in the array of potential C-termini acceptors INXYZH stores indices into ARXYZH for all donors MAXAMB is the maximum number of ambiguities MAXDON is the maximum number of donor IATs we can store MAXFFX is the maximum number of coupled-fixed configurations MAXFIX is the maximum number of coupled-fixed residues MAXH2D is the number of H positions for water MAXH2N is the maximum number of neighbouring conformations for h2o MAXH2P is the number of H position pairs for water MAXHAT is the maximum number of donated H-atoms we store MAXHGR is the maximum number of hydrogen bond donor groups MAXPLU is the maximum number of positively charged 1 atom drugs MAXSNS is the maximum subnet size MAXTAD is the maximum total number of affected donors MAXTPA is the maximum total number of potential acceptors MAXWHB is the maximum number of "WANTED" hydrogen bonds. METPEN penalty to be added when H approaches a metal. NAMB1 stores the index of the last residue ambiguity NAMB2 stores the index of the last ambiguity NUAD stores the number of affected donors for the ambiguity. NUDON stores the number of donors in the residue NUMDON stores the number of donors NUMFFX stores the number of coupled-fixed configurations NUMFIX stores the number of coupled-fixed ambiguities NUMHAR stores the total number of H atoms NUMHGR stores the number of hydrogen bond donor groups NUMPLU stores the number of positive one-atom drugs NUMTAD stores the total number of affected donors NUMTPA stores the number of potential acceptors NUMTT stores the number of donor to TER pointers NUMWHB stores the number of explicitly wanted hydrogen bonds. NUPA stores the number of potential acceptors NUTT stores the number of potential acceptors C-termini acceptors NUXYZH stores the number of H atoms in ARXYZH for all donors PENGRP stores the number of C-terminal oxygen atoms PLUSAT remembers the IAT-s of positive charges TOTPEN stores the total penalty for H atoms pointing to '+'-charge. TOTVAL stores the total donor value WHBFAC is the factor used to amplify wanted hydrogen bonds HB2FFX stores fixed conformations *CELLM : CELL DIMENSION ALONG A, B, OR C AXIS A1NAME : AS AANAME BUT NOW NOT IN 3- BUT IN 1-LETTER CODE AAFREQ : FREQUENCY OF OCCURENCE OF AMINO ACIDS AAISOK : LOGICAL. TRUE IF THE AA WAS OK UPON READING. AANAME : NAMES-LIST IN WHICH AASNUM FINDS THE NAMES OF THE AA AAPAIR : FREQUENCY MATRIX OF PAIRS OF AMINO ACIDS ACCCNT NUMBER OF TIMES AN ATOM IS AS ACCEPTOR IN A HBOND (PER ATOM) ACCDON : LOGICAL INDICATING WHETHER ACCESSIBILITY CALCULATION IS DONE ACCESS : ACCESSIBILITY FRACTION FOR ATOMS ACCUSD FLAG PER ATOM FOR ACCEPTORS USED IN HBOND OR NOT ACDEAA : LIST OF ON-LINE DEFINED SELF-MADE AMINO ACID POINTERS ACONVC COORDINATES OF CA OF CENTER OF SCREEN ALLGRD : ONE DIMENSIONAL INTEGER*2 ARRAY FOR EASY ALIGNMENT ALLMAT : ARRAY WITH ALL NEIGHBOUR MATRICES ALLSEQ : ARRAY CONTAINING ALL SEQUENCES ALPHAM : ALPHA ANGLE OF CELL ALREDY ? ANGERA ERROR OVER THE ACCEPTOR FOR EACH HBOND ANGERH ERROR OVER THE HYDROGEN FOR EACH HBOND ASMEAA : NAME OF ON-LINE DEFINED SELF-MADE AMINO ACID ATCOLR : ALSO HERE: COLOR OF ATOM (=REFLECTION) ATCOLR : COLOUR PER ATOM (0-360) ATORAA : LOGICAL. TRUE IF ROW IS FOR ATOMS, FALSE FOR AA. ATPRAA : THE NUMBER OF ATOMS THAT SHOULD BE PRESENT PER RESIDUE ATTVAL : ARRAY WITH SCRATCH ATOM RELATED VALUES BETAM : BETA ANGLE OF CELL BOTCNT NUMBER OF TIMES AN ATOM IS AS DON AND ACC IN HBOND (PER ATOM) BOTTOM_NEURONS NEURONS BETWEEN HIDDEN LAYER AND OUTPUT UNIT BPLANE : ARRAY WITH DIRECT-ACTION RESIDUES BRAVAIS: Bravais type of the conventional cell BUTTONS : LOGICAL ARRAY TO HOLD ON/OFF STATUS OF SCREEN BOTTOM BUTTONS CACA1 : CA-CA DISTANCES IN THE FIRST RANGE CACA2 : CA-CA DISTANCES IN THE SECOND RANGE CCELDIM: The 6 cell dimensions of the conventional cell CCLASS : CLASS of the conventional cell CELDIM : The 6 cell dimensions as read from the CRYST1 CELDIMS: The 6 cell dimensions as deduced from the SCALE? CELFND : Valid CRYST1 card found on input? CELREAD: CRYST1 card read from input? CELTR : Transformation to make cell input ---> conventional CELTRC : Transformation to make cell reduced ---> conventional CELTRR : Transformation to make cell input ---> reduced CHAINN CHAIN POINTER FOR RESIDUES CHARGE : ATOMIC PARTIAL CHARGES CHIANG : ARRAY WITH ALL CHI ANGLES FOR THE MAIN SEQUENCE CHICON : POINTERS TO CONNECTED ATOMS FOR CHIANGLES CHIUSE : NUMBER OF USABLE CHI ANGLES PER AMINO ACID CLASS : The crystal class of the cell on the CRYST1 card CLASS2 : The crystal class of the space group CLUNAM : NAMES GIVEN TO CLUSTERS CLUSTR : INDEX NUMBER IN MAIN SEQUENCE OF RESIDUES IN CLUSTER COMLST : FULL TEXT PLUS HELP FOR OLD STYLE COMMANDS COMMAA : MATRIX IN 10 DEGREE STEPS FOR ALLOWED NORMAL AA PHI-PSI'S COMTEXT : TEXT IN NEW-TYPE PULLDOWN MENUS CUTFLG : FLAG OF RESIDUES DIRECTLY BEFORE A CUT CYSCYS : POINTERS TO THE CYS-CYS AMINO ACIDS DATA_WEIGHT WEIGHTS ON THE TEST_DATA POINTS DATCOL : DATABASE ATOM COLOURS DEBUG DEBUG FLAG DEMOTX : HELP TEXT FOR DEMOS AND DIALOG BOXES DGMAT : MATRICES NEEDED TO MATCH DATABASE HITS ON THE STRUCTURE DGVEC : VECTORS BELONGING WITH DGMAT DGWHER : CONTAINS INFO ABOUT WHERE THIS GROUP MATCHES THE STRUCTURE DGWVAL : WEIGHTS USED ON DGLOOP CA'S DIFTMP : CA DIFFERENCES AFTER SUPPOS DONACD DONOR ACCEPTOR DISTANCE FOR EACH HBOND DONCNT NUMBER OF TIMES AN ATOM IS AS DONOR IN A HBOND (PER ATOM) DONUSD FLAG PER ATOM FOR DONORS USED IN HBOND OR NOT DSTCON : DISTANCES CORRESPONDING TO THE BONDS IN MUTCON DUBDUB FLAG PER ATOM FOR TWO HBONDS BETWEEN SAME DONOR AND ACCEPTOR DUBUSD FLAG PER ATOM FOR DON/ACC'S FOUND IN A HBOND ERRUNT IS THE UNIT WHERE REAL HARD ERRORS WILL BE LOGGED ETERMS : ENERGY TERMS PER ATOM ETMNAM : NAMES OF THE ENERGY TERMS ETMTOT : ENERGY TERMS PER RESIDUE FACT1 WEIGHT ON BOND LENGTHS FACT2 WEIGHT ON BOND ANGLES FACT3 WEIGHT ON TORSION ANGLES FACT4 WEIGHT ON PLANARITIES FAMILY : POINTERS TO FIRST AND LAST AA OF FAMILY IN MAIN SEQUENCE FAMNAM : NAMES GIVEN TO FAMILIES FBRTIRI : COORDINATES OF (CENTER OF) FBRT OBJECT FILCNM : CONVERTED NAMES OF THE PROTEINS IN DB (PDB 4 LETTER CODE) FILNMS : NAMES OF FILES TO BE USED FIX* : FLAG TO DETERMINE HOW TO SET ENVELOP POINT UPON TOGGLING FRCCYS : USER FORCED CYS-CYS PAIRS FTCRDS : CA COORDINATES OF STRETCH FOR WHICH BEST FIT IS WANTED FUDGE3 : PRETEND THAT THERE IS A PS300 GAMMAM : GAMMA ANGLE OF CELL GLYCIN : AS COMAA, BUT NOW FOR GLYCINES GRID : ELECTRON DENSITY GRID POINTS (INTEGER*2) GRID2 : ELECTRON DENSITY GRID POINTS (REALS) GRID2* : SMALLER ELECTRON DENSITY MAPS (2 MAPS) GRPACT : (BOOLS) INDICATORS FOR ACTIVE GROUPS GRPHOW : (CHAR80) TELL HOW GROUPS WERE MADE GRPLEN : LENGTHS OF GROUPS GRPNT2 : SECOND POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS GRPNT3 : THIRD POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS GRPNT4 : FOURTH POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS GRPNTR : POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS HARD_LIMIT EXTREME ABSOLUTE VALUE FOR NEURONS HBOCNT NUMBER OF HYDROGEN BONDS PER ATOM HBOPAR : DONOR=1; ACCEPTOR=-1; BOTH OR NOTHING=0 HBOPOS : TRUE/FALSE FOR POSSIBLE H-BOND PARTNER PER ATOM TYPE HBOTYP : CLASS OF HYDROGEN BOND DONOR/ACCEPTOR HBOUSD FLAG PER ATOM FOR USED IN HBOND OR NOT HINDX : MILLER INDEX H HISTOR : ARRAY HOLDING THE HISTORY OF COMPLETED OPERATIONS HKLUSE : IS REFLECTION PRESENT IN MDF? HSTQUA DSSP DETERMINATION FOR CENTER RESIDUE IN QUALITY CONTROL FILE HUEVAL COLOUR OF VECTORS IN XMOL AND YMOL HYDACD HYDROGEN ACCEPTOR DISTANCE FOR EACH HBOND ICOFDB : HASH TABLE FOR DRUGS IN THE ALDRUG.XYZ FILE IDEBUG : FLAG FOR DEBUG OUTPUT: 0 NO OUTPUT; 1 ALL OUTPUT IDEBUG : FLAG WHICH SETS AMOUNT OF DEBUG INFO (0=NOTHING) IDGSRT : INTEGER POINTER TO SORTED DGLOOP GROUP IDONE : STORES THE FRAGMENTS IN THE TWO RANGES IH2ODB : HASH TABLE FOR WATER IN THE ALDRUG.XYZ FILE ILVNOW : MAP LEVEL PRESENTLY BEING CONTOURED INCLUDE COMMON BLOCK FOR QUALITY BOXES INCLUDE FILE FOR DNA REGULARIZATION INCLUDE FILE SPECIFIC FOR (GROMOS) TRAJECTORIES INDSUP : INDICES TO MATRIX FILE NAMES INDTYP : PICK INDEX TYPE IN FILE 19 INDXCA : POINTER ROW TO LOCATIONS IN CA-CA DISTANCE FILE INPUT_LAYER ARRAY USED AS INPUT LAYER INWDTH NUMBER OF INPUT NODES USED IOBJ : ARRAY TO HOLD THE STATUS OF SG OBJECTS (ZERO=OFF) IPLUS : ADDITIVE VALUE TO GO FROM USER INPUT LEVEL TO INT*2 LEVEL IPLVEC LOGICAL ARRAY NEEDED FOR SENDING VECTOR LISTS TO PS300 IRFBRT : LOGICAL TO HOLD FBRT STATUS IRICC : ARRAY TO HOLD THE STATUS OF PICK BUTTONS IN VERTICAL SCREEN MENU IRISFLAGS: ARRAY WITH DEVICE STATUS PARAMETERS IRROCK : LOGICAL TO HOLD ROCKING STATUS IRSTAT : ARRAY WITH STATUS FLAGS FOR INTER-ROUTINE COMMUNICATION IRSTER : LOGICAL TO HOLD STEREO STATUS ISATOK : FLAG, TRUE IF THE ATOM IS OK, AND SHOULD BE CONSIDDERED ISET12345 : SETS OF EQUIVALENCED RESIDUES ISHBO1 LOGICAL IN COMMON FOR COMMUNICATION BETWEEN HBOND ROUTINES ISHBO2 LOGICAL IN COMMON FOR COMMUNICATION BETWEEN HBOND ROUTINES JUNIOR : WHAT IF JUNIOR IS BEING USED KINDX : MILLER INDEX K LABTXT : TEXT TO BE WRITTEN NEXT TO LABELED ATOMS LAWDTH WIDTH OF THE HIDDEN LAYERS LAYERS NUMBER OF HIDDEN LAYERS LENEAA : THE GROUPSIZE OF SELF DEFINED AMINO ACIDS LENGTH : LENGTH OF THE MATCHING FRAGMENT STARTING AT POSITION IAA LINDX : MILLER INDEX L LINE : CHARACTER*80 FOR TEMPORARY STORAGE OF CARD IMMAGES LLCNET : AS LOCNET, BUT NOW FOR A WHOLE SEARCH STRING LLCPAT : AS LOCPAT, BUT NOW FOR A WHOLE SEARCH STRING LOCHST DSSP DETERMINATION FOR THE RESIDUE LOCNEG : AS LOCNEI, BUT NOW FOR A WHOLE SEARCH STRING LOCNEI : AS LOCPAA, BUT NOW FOR OTHER RESIDUES (EG NEIGHBOURS) LOCNET : AS LOCPAT, BUT NOW FOR OTHER ATOMS (EG NEIGHBOURS) LOCPAA : BOOLEANS SET TO TRUE IF A CERTAIN RESIDUE SHOULD BE USED LOCPAT : BOOLEANS SET TO TRUE IF A CERTAIN ATOM SHOULD BE USED LOCPIG : AS LOCPAA, BUT NOW FOR A WHOLE SEARCH STRING LOGA : POINTERS TO DOTS ON THE SURFACE LOOKAT FLAG PER ATOM THAT IS LOOKED AT IN HBOND DETERMINATION MAPACT : SHOULD THIS MAP BE CONTOURED OR NOT MAPLEV : CONTOUR LEVELS OF MAPS IN REAL VALUES MAPMAX : HIGHEST VALUE IN MAP MAPMIN : LOWEST VALUE IN MAP MAPNAM : NAME OF MAP FILES MAPNOW : PRESENTLY ACTIVE MAP (=DEFAULT MAP) MAPNUM : NUMBER OF MAPS PRESENTLY KNOWN TO WHAT IF MAPORG : GRID COORDINATES OF FIRST POINT TO BE SHOWN MAPTXT : USER NOTES WITH THESE MAPS MAPTYP : 1 = INTERNAL ORTHOGONAL MAP MAPWID : EXTEND OF PORTION TO BE SHOWN MATEAA : THE MATRIX CONTAINING THE SELF DEFINED AMINO AMINO ACIDS MAXAA : MAXIMAL NUMBER OF AA ALLOWED IN THE SOUP MAXADB : MAXIMAL NUMBER OF RESIDUES PER SEQUENCE ALLOWED IN DATABASE MAXALI : MAXIMAL NUMBER OF RESIDUES PER SEQUENCE ALIGNMENT MAXAT : MAXIMAL NUMBER OT ATOMS ALLOWED PER STRUCTURE MAXBOX : NUMBER OF GRIDPOINTS PER SIDE OF PROPERTY/QUALITY BOXES MAXCCH : MAXIMAL NUMBER OF MULTI LINGUAL LINES TO BE CACHED MAXCLL : MAXIMAL NUMBER OF CLUSTERS MAXCLM : MAXIMAL NUMBER COLUMNS TO BE USED MAXCLU : MAXIMAL NUMBER OF AMINO ACIDS PER CLUSTERS MAXCMD : MAXIMAL NUMBER OF PULL-DOWN COMMANDS MAXCON : MAXIMAL NUMBER OF CONNECTIVITIES IN DRUGS MAXCYS : MAXIMAL NUMBER OF CYSTEINES IN THE SOUP MAXDG : MAXIMAL NUMBER OF DGLOOP HITS ALLOWED TO BE STORED MAXDG : MAXIMALLY ALLOWED NUMBER OF DG HITS TO BE STORED MAXEAA : MAXIMAL NUMBER OF SELF MADE AMINO ACIDS MAXETM : MAXIMAL NUMBER OF ENERGY CONTRIBUTIONS PER ATOM MAXETM : MAXIMAL NUMBER OF ENERGY TERMS PER ATOM OR RESIDUE MAXFAM : MAXIMAL NUMBER OF ALLOWED FAMILIES MAXG10 : DIMENSION OF THE TEN VERY SMALL MAPS MAXG2 : DIMENSION OF THE TWO MEDIUM SIZE MAPS MAXG4 : DIMENSION OF THE FOUR SMALL MAPS MAXGR2 : DIMENSION OF EQUAL SPACE MAP IN REALS MAXGRD : DIMENSION OF THE MAP IN INTEGERS*2 MAXIG : MAXIMAL NUMBER OF RESIDUES PER SUBGROUP MAXIOB : MAXIMAL NUMBER OF SG DRAWABLE OBJECTS MAXITM : MAXIMAL NUMBER OF MOL-ITEMS PER MOL-OBJECT MAXLAB : MAXIMAL NUMBER OF LABELS VISIBLE AT THE GRAPHICS MAXLAY MAXIMAL NUMBER OF HIDDEN LAYERS MAXLEV : MAXIMAL NUMBER OF CONTOUR LEVELS PER MAP MAXLLN : MAXIMAL LENGTH OF LABELS VISIBLE AT THE GRAPHICS MAXMAP : MAXIMAL NUMBER OF USABLE MAPS MAXMOL : MAXIMAL NUMBER OF MOLECULES IN THE SOUP MAXMOL MAXIMAL NUMBER OF NON-H2O MOLECULES IN THE SOUP MAXNDT MAXIMAL NUMBER OF DATA POINTS MAXNEI : MAXIMAL NUMBER OF NEIGHBOURS POSSIBLE PER RESIDUE MAXNEU MAXIMAL NUMBER OF NODES IN INPUT/HIDDEN LAYERS MAXOPT MAXIMAL NUMBER OF OPTIONS IN A MENU MAXPFL : MAXIMAL LENGTH OF A PIR FILE (INCLUDING DELETIONS) MAXPFS : MAXIMAL NUMBER OF PIR-FILES WHAT IF KNOWS OF MAXPRP : MAXIMAL NUMBER OF PARAMETERS PER PARALLEL SEQUENCE MAXPST : MAXIMAL NUMBER OF CUT AND PASTE FLAGS MAXPST MAXIMAL NUMBER OF CHAIN PASTE`S MAXQUA MAXIMAL VALUE IN QUALITY CONTROL FILE BEFORE SCALING MAXRDG : MAXIMAL NUMBER OF STEPS IN MOVIE OPTION(S) MAXSEQ : MAXIMAL NUMBER OF ENTRIES IN THE PROTEIN DATABASE MAXSP : MAXIMAL NUMBER OF SUBGROUP ADDRESS POINTERS MAXSUP : MAXIMAL NUMBER OF SUPERPOSITIONINGS WHAT IF CAN REMEMBER MAXSYM : Maximal number of allowed matrices MAXTAT : MAXIMAL NUMBER OF ATOMS THAT MOVES UPON ONE TORSION MAXTOR : MAXIMAL NUMBER OF TORSION ANGLES PER 'RESIDUE' MAXVEC : MAXIMAL NUMBER OF VECTORS ALLOWED PER GRAPHICS ITEM MENUPS NUMBER OF THE PSMENU TO BE SHOWN MITEMS POINTERS TO THE INSTANCES FOR MOL-ITEMS IN A MOL-OBJECT MITEXT NAMES OF THE MOL-ITEMS MITNUM NUMBER OF MOL-ITEMS USED PER MOL-OBJECT MOUSACT : NUMBER OF THE PRESENT SET OF MOUSE ACTIONS MPCOLR : COLOURS FOR ALL LEVELS OF THE MAP MPRIME : Matrix that rotates the cell into place. MPRIMS : Status of the last matrix MUTCON : ORDER OF CONNECTIONS IN MUTROW MUTDAT.INC CONTAINS THE AMINO ACID NAMES ETCETERA AND MUTROW : ATOM NAMES STORED IN MAXTAT*CHAR*4 PER RESIDUE MXGDCB : TOTAL (LINEAR) SIZE OF THE GRID SPACE MXQBOX MAXIMAL NUMBER OF ATOM BOXES PER BOX FILE MXQBSZ DIMENSION OF ONE INDIVIDUAL BOX MXQIAT TOTAL NUMBER OF POSSIBLE ATOMS (20 RES.+/- 8 ATOMS) MXQUAT TOTAL NUMBER OF PACKED ATOMS MY_MENU : COMMANDS IN THE PERSONAL MENU M_P : MAXIMAL ATOM PICK INDEX (M_P==-MAXATM) N* : NUMBER OF GRIDPOINTS IN U, V, OR W DIRECTION NAAFIL : NUMBER OF AMINO ACIDS PER PROTEIN NAMFIL : NAMES OF THE PROTEINS IN DB (PDB 4 LETTER CODE) NATFIL : NUMBER OF ATOMS PER PROTEIN NBINDB : NUMBER OF ENTRIES FOUND IN DATABASE NDIV* : NUMBER OF MAP DIVISIONS IN A, B, OR C DIRECTION NEADST : All matrices that generate contacts less than NEADST are NEURONS NEURONS BETWEEN HIDDEN LAYERS NEURON_FLAG FLAGS FOR COMMUNICATION BETWEEN NEURAL NETWORK ROUTINES NEWCLS : Logical indicating that the conventional cell has a NEXT CHARACTER STRING (LABTXT) SHOULD BE MAXLLN LONG NMGRFN : NUMBER OF GROUPS FOUND NODES ARRAY TO STORE HIDDEN NODES NOMAIN : FLAG THAT TELLS WHETHER THERE IS A MAIN SEQUENCE READ IN OR NOT NOTUNT IS FOR NOTES, INFO, STATISTICS, ETC. NP1 : COLUMN NUMBER OF READ COLUMN 1 NP2 : COLUMN NUMBER OF READ COLUMN 2 NP3 : COLUMN NUMBER OF READ COLUMN 3 NP4 : COLUMN NUMBER OF READ COLUMN 4 NPP : NP1 TILL NP4 NUMAAF : NUMBER OF AA FOUND IN SEQUENCE NUMAAT : NUMBER OF RESIDUES FOUND IN SOUP NUMAT : MAXIMAL NUMBER OF DIFFERENT ATOM TYPES ALLOWED NUMATF : NUMBER OF ATOMS PRESENT NUMBUF : NUMBER OF VECTORS CREATED FOR MAP NUMCOF : NUMBER OF COFACTORS NUMCYS : NUMBER OF CYS-CYS PAIRS NUMEAA : THE NUMBER OF SELF DEFINED AMINO ACIDS NUMH2O NUMBER OF SOLVENT MOLECULES IN THE SOUP NUMNAM : NUMBER OF AMINO ACID ACCORDING TO NOMENCLATURE NUMOPT ACTUAL NUMBER OF OPTIONS NUMRNG NUMBER OF RESIDUES IN REQUESTED RANGE NUMROW : NUMBER OF HITS IN EACH ROW NUMSOU NUMBER OF MOLECULES IN THE SOUP NUMSTS TOTAL NUMBER OF HBONDS NUMSUP : NUMBER OF PRESENTLY KNOWN MATRICES NUMSYM : Number of available symmetry matrices NUMTAB : NUMBER OF TABLES IN USE NUMUA : MAXIMAL NUMBER OF DIFFERENT AA ULTIMATELY ALLOWED NUMUT : OVERALL NUMBER OF ATOM TYPES FOUND SO FAR NXTGRP : NUMBER OF THE NEXT FREE GROUP NXTROW : NUMBER OF NEXT FREE ROW NXTSEL NUMBER OF NEXT FREE COLUMN ONESA1 : RESIDUE IN ONE LETTER CODE ONESA3 : RESIDUE NAME IN THREE LETTER CODE ONESAT : ATOM TYPES FOR ATOMS PRESENT IN 4-LETTER CODE OPTION OPTION SET ORGNAM : ORIGINAL PDB NAME IN CASE ATOMS IN ONE UNIT HAVE ORTMAT : OFTEN USED MATRIX FOR ORTHOGONALISATION PURPOSES PCKLST COORDINATES OF LAST PICKED ATOM PDBUNT IS THE UNIT NUMBER WHERE ERRORS WARNINGS ETC WILL BE WRITTEN PIRDAT : ARRAY WITH SEQUENCES IN ONE LETTER CODE (IN ESPACE!) PIRFLS : FILE NAMES OF PIR FILES PNTAAC : POINTER TO CA'S IN ATOM TYPE ARRAYS PNTAAE : POINTER TO END OF AA IN ATOM TYPE ARRAYS PNTAAS : POINTER TO START OF AA IN ATOM TYPE ARRAYS POPTXT : STATUS FLAGS FOR PULL-DOWN MENU OPTIONS PRESOU : MOLECULE NUMBER ON WHICH LAST PREGRO HAS RUN PROD : MULTIPLIER TO GO FROM USER INPUT LEVEL TO INTEGER*2 LEVEL PROGRAM NEEDS TO BE RECOMPILED!! PLEASE CHECK CAREFULLY FOR PARAMETER PSTFLG : FLAG OF RESIDUES DIRECTLY BEFORE A PASTE QDONE : STORES THE Q-RMS FOR THE MATCHED FRAGMENTS IN IDONE QFACTS : FIT QUALITY FACTORS FOR THE OBSERVED FITTED STRETCHES QFCSTR : SORTED QUALITY OF FIT FACTORS QUALBL SIGNIFICANT PART OF QUALBY QUALBX QUALLITY BOXES STORED AS INTEGER*2 QUALBY QUALITY BOXES STORED AS BYTES RCELDIM: The 6 cell dimensions of the reduced cell RECRD : SCRATCH ARRAY TO READ COORDINATES PER AA FROM DATA BASE RESREF : RESOLUTION OF THIS REFLECTION (H,K,L) RESTYP : INTEGER REPRESENTATION OF ONESA3 ROCKANGLE: MAXIMAL ROCKING ANGLE ROCKDYNOW: PRESENT ROCK ANGLE ROCKSPEED: ANGLE PER ROCK-STEP ROW123 : LOGICAL ROWS FOR STORAGE OF THE SEARCH ROWS ROWTXT : TEXT CREATED WITH THE ROWS ROWUSE : LOGICAL THAT TELLS IF THE ROW IS ON OR NOT SCLFND : Valid scale card found on input? SCLREAD: Scale card read from input? SECOND BLOCK IS MORE NEEDED FOR NORMAL, PAIRWISE SUPPOS SELCHC CONTACT CHANCE FOR AMINO ACIDS IN SELECTED PROTEINS SELCLM ARRAY WITH ALL COLUMNS IN IT SELNAM ARRAY WITH THE TITLES OF THE COLUMNS SELUSE ARRAY WITH FLAGS FOR USED/NON-USED COLUMNS SHORT_CUT FLAG FOR SPEED PURPOSES IN CASE OF LARGE DATASETS SHOULD THEN ONLY BE USED IN THE MAIN PROGRAM. SOFT_LIMIT PREFERRED EXTREME ABSOLUTE VALUE FOR NEURONS SOUADM ADMINISTRATION OF CHAIN TYPE/CONTENTS SOUNAM NAME OF THIS MOLECULE IN THE SOUP SOUPNT : POINTER FROM RESIDUE TO SOUNAM TABLE SOURNG RANGE OF REQUESTED RESIDUES FOR USER IO SPCNAM : Name of the space group SPCNUM : Number of the present spacegroup SPHRAD : CENTER AND RADIUS OF SMALLEST SPHERE AROUND THE RESIDUE STEP* : STEP SIZE IN THE U, V, OR W DIRECTION STEP_SIZE MAXIMAL CHANGE OF A NEURON PER TRIAL STNDIS STANDARD BOND LENGTHS (PARALLEL WITH MUT***) SUMACC : TOTAL ACCESSIBLE SURFACE AREA PER RESIDUE SUPMAT : ONE SUPERPOSITION MATRIX IN COMMON SUPNAM : NAMES OF MATRIX FILES SUPVEC : THE ACCOMPANYING SUPERPOSITION TRANSLATION VECTOR SYMAL1 : The first of the two inconsistent scale matrices SYMAL2 : The second of the two inconsistent scale matrices SYMALT : There are two inconsistent scale matrices available SYMGCA : If true: show only CA in mol-items created by sym SYMMAT : Symmetry matrices SYMNIN : Index of inverse transformation SYMSTS : The type of symmetry matrix SYMVEC : Translational components of symmat TABLEN : ARRAY WITH LENGTHS OF TABLES TABNAM : NAMES OF TABLES TABTYP : TYPE OF TABLE TO BE USED TABUSE : LIST OF TABLES ACTIVATED BY THE USER TEST_ANSWERS DESIRED OUTPUTS (BINDING CONSTANTS) TEST_DATA POINTS IN THE DATA SET TEST_SET_LENGTH ACTUAL NUMBER OF DATA POINTS IN DATA SET TOPTXT : TEXT TO BE WRITTEN IN TOP-RIGHT CORNER OF SCREEN TOP_NEURONS NEURONS BETWEEN TOP AND HIDDEN LAYER TORANG : ARRAY WITH ALL TOR ANGLES FOR THE MAIN SEQUENCE TORCON : POINTERS TO CONNECTED ATOMS FOR TORANGLES TPTXLN : FIRST INFO TEXT FOR DIALOG BOXES TPTXLN2 : SECOND INFO TEXT FOR DIALOG BOXES TRIGER : BOOLEAN TELLING WHICH REFS TO USE FOR GRAPHICS USE300 LOGICAL WHETHER PS300 IS ON OR NOT USEAT : LOGICAL TO FLAG USAGE OF ATOMS USESOU NUMBERS OF MOLECULES TO BE USED UVWMAT : MAP CONVERSION MATRICES UVWORG : ORIGIN OF THE MAPS IN FRACTIONAL COORDINATES V1 : VALUE FOUND IN MDF COLUMN 1 V2 : VALUE FOUND IN MDF COLUMN 2 V3 : VALUE FOUND IN MDF COLUMN 3 V4 : VALUE FOUND IN MDF COLUMN 4 VDDDON : TRUE IF VAN DER DOT FILE HAS BEEL GENERATED VDWRAD : VAN DER WAALS RADIUS OF ATOMS WARUNT WILL BE USED TO LOG WARNINGS WEIGHT : WEIGHT PUT ON ATOMS (TYPICAL X-RAY CRYSTALLOGRAFIC THING) WHAT IF CAN DEAL WITH. CHANGING ONE PARAMETER MEANS THAT THE WHOLE WHERIS : LOCATION (=DIRECTORY NAME) OF THE DATABASE FILES WIF072 FUNCTION TO CALCULATE DEPTH IN MENU TREE WIFFAC : INDICATES STATUS OF PROTEIN IN DATABASE WIFPAR : INTERNAL COUNTERS AND FLAGS (SEE PROGRAM DOCUMENTATION) WORKAA : AMINO ACID OF CENTER OF SCREEN WORKMAT : MATRIX FOR MANIPULATING/SAVING/RESTORING VIEW MATRIX WORKTF : BOOLEAN FOR RESIDUE ALREADY IN WORK OR NOT WRKREF : THE ACTIVE COPY OF V1-4 XBFACT : TEMPERATURE FACTORS FOR ATOMS XCOORD : X-COORDINATES FOR ATOMS XIDA : COORDINATES OF IDENTIFIER POSITIONS AT THE SCREEN XMOL COORDINATES OF START POINT OF GRAPHICS VECTOR XUACC : X-COORDINATES OF DOTS AT ACCESSIBILITY CALCULATION SURFACE XYZ : REAL(3) ARRAY FOR COORDINATE OPERATIONS (SCRATCH) XYZ1,2,3 : COORDINATES OF ALPHA CARBONS XYZCAS : COPY OF X,Y,Z COORDINATES OF CA'S (FOR GRAFICS MAINLY) YCOORD : Y-COORDINATES FOR ATOMS YMOL COORDINATES OF END POINT OF GRAPHICS VECTOR YUACC : Y-COORDINATES OF DOTS AT ACCESSIBILITY CALCULATION SURFACE ZCOORD : Z-COORDINATES FOR ATOMS ZUACC : Z-COORDINATES OF DOTS AT ACCESSIBILITY CALCULATION SURFACE
The topology file should start with N amino acids (N should be given in ICONFI.FIG, sorry). Thereafter DNA/RNA should follow, and the file should be closed with the drugs for which a topology has been user-added.
Per amino acid the following information has to be present: 1) An asterix 2) The name in three and 1 letter code (A4,A1 left justified) 3) Seven constants that indicate: (Free format integers) 1) The number of atoms (ATPRAA) 2) The number of intra-residue bonds 3) The number of rotable side-chain torsion angles (CHIUSE) 4) The number of measurable torsion angles 5) 1 -> Standard atomic coordinates are present ( 0 -> not ) 6) Standard bondlengths for the first N bonds 7) Number of hydrogen bond 'groups' 4) The atom names (14A4 left justified) 5) Pairs of bonded atoms (10 pairs of integers per line, free format) 6) Per rotable side-chain: the two atoms that define the axis followed by all atoms that should rotate (20 integers per line, free format) 7) Per measurable torsion angle the four atoms (20 free format integers per line; that is 5 torsion angles per line) 8) Per atom the following information: 1) Standard X coordinate \ 2) Standard Y coordinate |-> free formatted within columns 1-29 3) Standard Z coordinate / 4) T or F for hydrogen bondable or not. Fixed in column 30. 5) + or - for donor or acceptor (blank means both possible) Fixed in column 31 6) Hydrogen bond type number. Fixed column 33. 7) Group number this donor/acceptor is member of. Fixed column 35. 9) The standard bondlengths (one per line, free format) 10) Number of hydrogen bond groups, followed by per group ???? I5,30F5.2
* GLU E 15 14 3 3 1 8 1 N CA C O CB CG CD OE1 OE2 1N 1CA 1CB 2CB 1CG 2CG 1 2 2 3 3 4 2 5 5 6 6 7 7 8 7 9 1 10 2 11 5 12 5 13 6 14 6 15 2 5 6 7 8 9 12 13 14 15 5 6 7 8 9 14 15 6 7 8 9 1 2 5 6 2 5 6 7 5 6 7 8 1.20131 0.84661 0.00001 T+ 1 0.00001 0.00001 0.00001 F -1.25031 0.88111 0.00001 F -2.18531 0.66031 -0.78411 T- -0.05931 -0.87451 1.25831 F 1.08171 -1.84981 1.50081 F 0.98981 -2.68741 2.73981 F 0.06741 -2.62371 3.53931 T 7 1 1.97021 -3.44941 2.87091 T 7 1 1.20131 1.84661 0.00001 F 0.00002 -0.58204 -0.81314 F -0.90302 -1.40913 1.21004 F -0.09876 -0.26025 2.04643 F 1.92852 -1.32051 1.55339 F 1.12423 -2.46941 0.71704 F 1.453 1.530 1.230 1.530 1.530 1.530 1.265 1.265 2 0.00 0.75 9.99