Program parameters

Introduction

At many places in WHAT IF term like 'nearby', or 'a certain precission' are being used. In all these cases there is of course a well defined parameter value involved. For all these parameters there are sensibily choosen defaults. You can however change these parameters if you want.

In many menu's you find the command PARAMS. This command will always bring you in the menu from which you can change the parameters relevant to menu you just came from.

The command SETPAR brings you in a menu from which you can go to many sub-menu's, each of which allow for the (re-)setting of some of the internal parameters that belong to a certain kind of option.

List of parameters

All parameters in WHAT IF are internally stored as integers. Reals are simply multiplied by 100 or 1000, and divided back before usage. The parameters ar stored in the array WIFPAR.

The command SETWIF allows you to poke a value in this array. With this command you can circumvent WHAT IF's artificial stupidity (AI) that is ivoked to check your parameter choice....

At 17-7-1995 the parameter list looked like:


   1       One or three letter code flag for listing amino acids 
     = 0   1 letter code                  
     = 1   3 letter code                  
                                          
   2       Amount of sequence information 
     = 0   only sequence                  
     = 1   sequence + aa frequency        
     = 2   sequence + frequency + neighbor matrix  
                                          
   3       Scale factor for arrows (*100) 

   4       The number of the one indicated database file to work with 
                                          
   5       Output in debump flag         
     = 0   Do not give output (unless other falg says to do so)     
     = 1   Do always give output
 
   6       Precision of accessibility calculation  
     = 0   Very course                    
     = 1   Course                         
     = 2   Normal (default)               
     = 3   Fine                           
     = 4   Very fine                      
                                          
   7       Repeat angle for property moment calculations 
           default = 100 (helix)          
                                          
   8       Moving average box width in property moment calculations   
           default = 17                   
                                          
   9       Property number for property moment calculations   
           default = 19 (hydrophobic moment)   
                                          
  10       Text in TOPTXT indicates error.
     = 0   No, normal text
     = 1   Yes there is an error
                                          
  11       Use protons in FCONATI etc routines             
     = 0   Use protons 
     = 1   Do NOT use protons 
                                          
  12       Use the database etc      
     = 0   Open all data base files upon startup of WHAT IF
     = 1   Do NOT open any data base files upon startup of WHAT IF
                                          
  13       Set NUMGRV to zero in character output  
     = 0   Set NUMGRV every time to zero in CHR000 (default)   
     = 1   Do NOT set NUMGRV to zero in CHR000 
                                          
  14       Automatic looping flag for SUPPOS (3SSP)
     = 0   Prompt user where ever needed  
     = 1   Always compare M1 with M2 automatically (for 3SSP) 
                                          
  15          
                                          
  16       NUMBER OF DEGREES PER STEP IN AUTOMATIC DENSITY FITTING 
                                          
  17       NUMBER OF STEPS PER TRY IN AUTOMATIC DENSITY FITTING    
                                          
  18       NUMBER OF HITS BELOW WHICH SLEEPING PROTEINS WILL BE USED  
           TOO IN THE SCNSEL OPTION OF THE SCAN3D MENU.  
                                          
  19       DENSITY FITTING AUTOMATION FLAG     
     = 0   ASK EVERY AA FOR THE DENSITY FITTING PARAMETERS    
     = 1   USE WIFPAR DERIVED DENSITY FITTING PARAMETERS 
                                          
  20       (100*) WIDTH OF THE STICK OF AN ARROW IN ANGSTROMS 
           DEFAULT=0.5                    
                                          
  21       (100*) LENGTH OF THE STICK OF AN ARROW IN ANGSTROMS     
           DEFAULT=2.5                    
                                          
  22       (100*) WIDTH OF THE POINT OF AN ARROW IN ANGSTROMS 
           DEFAULT=0.5                    
                                          
  23       (100*) LENGTH OF THE POINT OF AN ARROW IN ANGSTROMS     
           DEFAULT=1.0                    
                                          
  24       NUMBER OF SIDES OF AN ARROW    
           DEFAULT=6                      
                                          
  25       COLOUR OF AN ARROW             
           DEFAULT=170                    
                                          
  26       NEAREST NEIGHBOUR IN BUMPS AND CONTAC RUNS    
           DEFAULT=1 (MEANING DO NOT USE THE DIRECT NEIGHBOUR)  
                                          
  27       GRAPHICS FLAG IN CONTAC AND BUMPS   
     = 0   DO NOT SHOW DASHED LINES FOR CONTACTS AND BUMPS (DEFAULT) 
     <> 0  SHOW DASHED LINES FOR CONTACTS AND BUMPS 
                                          
  28       OUTPUT FLAG IN ACCESSIBILITY CALCULATIONS     
     = 0   DO NOT LIST WHAT IS BEING CALCULATED (DEFAULT)     
     <> 0  DO LIST WHAT IS BEING CALCULATED    
                                          
  29       RADIUS OF THE WATER PROBE IN ACCESSIBILITY CALCULATIONS 
           DEFAULT = 1.4 (*100)           
                                          
  30       MOVITM ITEM TYPE FLAG          
     = 0   MOVABLE ITEM CONSISTS OF LINES     
     = 1   MOVABLE ITEM CONSISTS OF DOTS 
                                          
  31       COLOUR OF DSSP DETERMINED 'H' RESIDUE    
  32       COLOUR OF DSSP DETERMINED '3' RESIDUE    
  33       COLOUR OF DSSP DETERMINED 'S' RESIDUE    
  34       COLOUR OF DSSP DETERMINED 'B' RESIDUE    
  35       COLOUR OF DSSP DETERMINED 'T' RESIDUE    
  36       COLOUR OF DSSP DETERMINED 'C' RESIDUE    
                                          
  37       COLOUR TO LINETYPE FLAG FOR OUTPUT PURPOSES   
     = 0   USE THE USER REQUESTED LINE TYPE FOR THE WHOLE PLOT     
     = 1   USE THE INTERNAL CONVERSION SCALE   
                                          
  38       LOWEST COLOUR IN COLOUR RANGES 
                                          
  39       HIGHEST COLOUR IN COLOUR RANGES     
                                          
  40       NUMBER OF TYPOS ALLOWED IN COMMANDS (DEFAULT=1)    
                                          
  41       FLAG TO DETERMINE HOW TO GROW IN THE BUILD MENU    
     = 0   DEFAULT EXTENSION (ROUGHLY SHEETISH)     
     = 1   USE SPECIAL ANGLES             
                                          
  42       PHI-ANGLE IN CASE PARAMETER 41 IS SET TO 1    
  43       PSI-ANGLE IN CASE PARAMETER 41 IS SET TO 1    
  44       OMEGA-ANGLE IN CASE PARAMETER 41 IS SET TO 1  
           IN CASE OF AN N-TERMINAL RESIDUE THE PHI-ANGLE IS APPLIED  
           TO THE NEXT RESIDUE. IN CASE OF A C-TERMINAL RESIDUE, THE  
           OMEGA- AND PSI-ANGLE ARE APPLIED TO THE PREVIOUS RESIDUE.  
                                          
  45       SALT BRIDGE CONTACT DISTANCE * 100.0 (5.0)    
                                          
  46       FLAG TO DETERMINE WHETHER OR NOT TO PUT CONSTRAINTS ON THE 
           NEIGHBOURS IN THE SCNCON/SCNGRN OPTION   
     = 0   DON'T PUT CONSTRAINTS ON THE NEIGHBOURS  
     = 1   DO PUT CONSTRAINTS ON THE NEIGHBOURS     
                                          
  47       FLAG TO DETERMINE WHETHER ONLY TO PROMPT FOR THE MIDDLE 
           RESIDUE OR FOR THE WHOLE STRETCH IN THE SCAN3D CONTACT  
           OPTIONS SCNCON, SCNGRN, SCNGRL, ETC.     
     = 0   ONLY PROMPT FOR THE MIDDLE ONE OF A STRETCH LENGTH FIVE 
     = 1   PROMPT FOR THE WHOLE STRETCH OF PREDEFINED LENGTH  
                                          
  48       INTERNAL PARAMETER HOLDING THE GROUP NUMBER FOR THE GROUP  
           PRESENTLY BEING SET. THIS PARAMETER CAN NOT BE SET BY THE  
           USER.                          
                                          
  49       ERROR LIMIT FOR DGCONT HITS TO ACCEPTED, DEFAULT=4 ANGSTROM.----
                                          
  50       FLAG FOR PLOT MODE OF DG*** HITS    
     = 0   ONLY SHOW BACKBONE + =O + C-BETA (DEFAULT)    
     = 1   SHOW THE WHOLE AMINO ACIDS     
           (THE CENTRAL HIT IS ALWAYS SHOWN COMPLETELY)  
                                          
  51       LENGTH OF SUBGROUPS TO SEARCH FOR   
     = 1   SEARCH FOR SINGLE AMINO ACIDS  
     = 2   SEARCH FOR PAIRS OF AMINO ACIDS     
     ...                                  
                                          
  52       100 * THE MAXIMAL ALLOWED ERROR IN CA POSITION IN DGLOOP   
           FITTING.                       
                                          
  53       100 * THE ALLOWED RMS ERROR IN THE TOTAL FIT IN DGLOOP  
           FITTING.                       
                                          
  54       COUNTS THE NUMBER OF HITS BY DGLOOP NOT USER DEFINABLE  
                                          
  55       NUMBER OF DGLOOP HITS TO BE USED/SHOWN.  
           DEFAULT = 20                   
                                          
  56       100 * THE VAN DER WAALS RADIUS OVERLAP LIMIT  
           DEFAULT = 0.25 ANGSTROM        
                                          
  57       DEFAULT B-FACTOR WHEN NO B-FACTOR IS PRESENT UPON READING  
           DEFAULT = 12                   
                                          
  58       DISTANCE BETWEEN PSEUDO SPHERES (*100) ALLOWED FOR TWO  
           RESIDUES TO BE CALLED NEIGHBOURS.   
           DEFAULT = 4.0 ANGSTROM         
                                          
  59       ALLOWED ACCESSIBLE SURFACE FOR `BURIED` RESIDUE OR ATOM 
           DEFAULT = 2 SQUARED ANGSTROM   
                                          
  60       MAXIMAL DONOR ACCEPTOR DISTANCE IN A H-BOND (*100) 
           DEFAULT = 3.5 ANGSTROM         
                                          
  61       MAXIMAL ANGULAR ERROR ALLOWED FOR A H-BOND    
           DEFAULT = 60 DEGREES           
                                          
  62       NEIGHBOUR TESTING FLAG         
     = 0   USE ALL ATOMS (=DEFAULT)       
     = 1   USE ONLY SIDECHAIN ATOMS       
     = 2   USE ONLY MAIN CHAIN ATOMS      
                                          
  63       MINIMAL NUMBER OF REQUIRED DG*** HITS TO CONTINUE. SEE THE 
           MANUAL FOR A LIST OF OPTIONS USING THIS FLAG. 
                                          
  64       ADDITIONAL BACKBONE FIT FLAG IN DG-REPLACE OPTIONS.     
     = 0   DO NOT PERFORM THE ADDITIONAL FIT.  
     = 3   PERFORM ADDITIONAL FIT ON N, CA, C. 
     = 4   PERFORM ADDITIONAL FIT ON N, CA, C, O.   
     = 5   PERFORM ADDITIONAL FIT ON N, CA, C, O, CB (IF PRESENT)  
                                          
  65       MAXIMAL ALLOWED DIFFERENCE BETWEEN ORIGINAL AND FITTED  
           CA POSITION (THUS AFTER REAL 3D SUPERPOSITION) *100.0   
                                          
  66       GRAPHICS OUTPUT FLAG. THIS FLAG DETERMINES WHAT ACTION IS  
           IS TAKEN WHEN THE COMMAND `GRAFIC` IS USED.   
     = 0   CREATE PS390 MOLITEM FILE      
     = 1   MAKE PLOT FILES                
                                          
  67       B-FACTOR CORRESPONDING TO RED IN CASE OF BFACTOR GRAPHICS  
                                          
  69       DETERMINES WHETHER HEADER CARDS READ FROM A PDB FILE    
           WILL BE SHOWN UPON READING OR NOT.  
     = 0   DO NOT SHOW THEM (DEFAULT)     
     = 1   DO SHOW THEM                   
                                          
  70       NUMBER OF ANCHOR AMINO ACIDS AT EITHER END OF AN INSERTION 
           OR DELETION IN THE DG**** MENU /OPTIONS. DEFAULT=3.     
                                          
  71       DEFAULT COLOR FOR LINES DRAWN AT THE GRAPHICS 
                                          
  72       MODE FOR LINES DRAWN AT THE GRAPHICS     
     = 0   CONTINUOUS LINES               
     = N   IN N DASHES (15=DEFAULT)       
                                          
  73       STEPS PER 360 DEGREES IN DEBUMPING. DEFAULT=3.     
                                          
  74       DEFAULT MAP RESOLUTION (*100). DEFAULT=2(00)  
                                          
  75       FLAG FOR RESETTING THE NUMBER OF STEPS PER CHI-ANGLE    
     = 0   ASK THE USER EVERY TIME AGAIN  
     = 1   USE THE DEFAULT, AND DO NOT ASK OR TELL THE USER     
                                          
  76       FLAG TO SKIP CHI-N IN DEBUMPING     
     = 0   SKIP NOTHING (DEFAULT)         
     = 1   SKIP CHI-1                     
     = 2   SKIP CHI-1 AND CHI-2           
     = 3   SKIP CHI-1 AND CHI-2 AND CHI-3 
                                          
  77       SPECIAL FLAG FOR SCNGRN IN THE SCAN3D MENU.   
     = 0   DO WRITE MOL ITEMS TO PS300 ALWAYS  
     = 1   DO NOT WRITE MOL-ITEMS TO THE GRAPHICS, BUT TO A FILE   
                                          
  78       MODE FLAG FOR EQUAL OPTION IN SUPPOS MENU     
     = 0   DEFAULT. DO NORMAL EQUAL. COLOUR AS F(MISFIT) 
     = 1   ASSUME SUPPOS IS DONE. COLOUR BY PROPERTY.    
                                          
  79       MODE FOR ACCESSIBILITY CALCULATION  
     = 0   (DEFAULT) GIVE CONTACT SURFACE 
     = 1   GIVE ACCESSIBLE SURFACE        
                                          
  80       MOL200 RUNS IN INPUT MODE OR UPDATE MODE 
     = 0   (DEFAULT) UPDATE MODE          
     = 1   INPUT MODE. THUS ATOMIC DISTANCES ARE CHECKED TOO 
                                          
  81       MINIMAL LENGTH OF STRETCH IN AUTO SUPPOS (DEFAULT=20)   
                                          
  82       MAXIMAL INDIVIDUAL ERROR IN AUTO SUPPOS (DEFAULT=100*3.8)  
                                          
  83       MAXIMAL RMS ERROR IN AUTO SUPPOS (DEFAULT=100*2.0) 
                                          
  84       DO WE USE HYDROGENS? 0=NO; 1=YES.   
                                          
  88       MAXIMAL ANGULAR ERROR IN MOTIVES (DEFAULT=5 DEGREES)    
                                          
  89       MAXIMAL TRANSLATIONAL ERROR IN MOTIVES   
           (DEFAULT=100.0*2.0 ANGSTROM)   
                                          
  90       CUTOFF DISTANCE FOR NAYB OPTION (DEFAULT=4.0(*100))     
                                          
  91       DEFAULT COLOUR FOR DOTTED NAYB OPTION LINES (DEFAULT=300)  
                                          
  92       SPHERE FOR PLUTO PICTURES (DEFAULT=0.5(*100)) 
                                          
  93       THICKNESS OF PLUTO BONDS (DEFAULT=0.1(*100))  
                                          
  94       NUMBER OF LINES IN PLUTO BONDS (DEFAULT=20)   
                                          
  95       SQUARE MODE FLAG IN DIAGONAL PLOTS  
     = 0   SQUARE SIDE LENGTH IS FUNCTION OF NUMBER OF ATOMS IN RESIDUE----
     = 1   ALL SQUARE SIDE LENGTHS WILL BE IDENTICAL     
                                          
  96       RESIDUE CORRECTION INPUT FLAG  
     = 0   NORMAL MODE. USE ALL 4 CHARACTERS OF RESIDUE NAME  
     = 1   FORCE 4-TH CHARACTER OF RESIDUE NAME TO BE BLANK UPON INPUT
                                          
  97       MINIMAL NUMBER OF NON-HELICAL RESIDUES IN MOTIF FRAGMENTS  
                                          
  98       OUTPUT IN 3SSP OPTION TO LOGFILE OR UNIT 6    
     = 0   DO NOT PRODUCE OUTPUT          
     = 1   DO PRODUCE OUTPUT              
                                          
  99       GROUP NUMBER FOR DGROTA RELATED GROUPS   
                                          
 100       LENGTH OF GROUP FOR IMPLICIT LOGICAL AND IN DGROTA OPTIONS 
                                          
 102       COLOUR OF FRAME IN CONTACT ANALYSIS 
                                          
 103       COLOUR OF SEQUENCES WRITTEN IN CONTACT ANALYSIS FRAME   
                                          
 104       COLOUR OF NEIGHBOUR RESIDUES IN CONTACT ANALYSIS   
                                          
 105       COLOUR FOR PICK LABELS IN CONTACT ANALYSIS    
                                          
 106       FLAG FOR PUTTING CA-CROSSES IN RESIDUE SQUARES IN ANACON   
     = 0   DO NOT PUT OUT CA CROSSES (DEFAULT)   
     = 1   DO PUT OUT CA CROSSES          
                                          
 107       THREE LETTER CODE IN FRAME FLAG     
     = 0   USE ONE LETTER CODE (DEFAULT)  
     = 1   USE THREE LETTER CODE          
                                          
 109       USE ONLY TOP HALF OF PLOT FLAG 
     = 0   USE FULL PLOT (DEFAULT)        
     = 1   USE ONLY TOP HALF              
                                          
 110       COLOUR OF CA CROSSES IN RESIDUE SQUARES IN CONTACT ANALYSIS
                                          
 111       ITEM LABEL OBJECT NAME FLAG    
     = 0   AUTOMATIC NAMING, UNPLOTTABLE  
     = 1   IMPLICIT NAMING, SLOWER, BUT PLOTTABLE   
                                          
 112       ANCHOR FLAG IN REFINE          
     = 0   DO NOT ANCHOR THE ENDS OF A REFINEMENT STRETCH     
     = 1   ANCHOR THE ENDS OF A REFINEMENT STRETCH  
                                          
 113       FLAG TO SEE SHIFTS AFTER REFINE     
     = 0   ASK THE USER IF HE WANTS TO SEE THE SHIFTS    
     = 1   DO NOT ASK THE USER, AND DO NOT SHOW THE SHIFTS   
                                          
 114-119   PARAMETERS RESERVED FOR REFINE 
                                          
 120       FLAG TO TELL WHAT IF THAT WE ARE IN PDB_CHECK MODE 
     =0    NOT IN CHECK MODE (SO, LITTLE OUTPUT)    
     =1    CHECK MODE ON (SO MUCH MORE OUTPUT) 
                                          
 121       USE DASHED BONDS IN GRAPHICS FLAG   
     = 0   DO NOT USE DASHED BONDS        
     = 1   USE DASHED BONDS               
                                          
 122       USE DOUBLE BONDS IN GRAPHICS FLAG   
     = 0   DO NOT USE DOUBLE BONDS        
     = 1   USE DOUBLE BONDS               
                                          
 123       CYS-CYS ADMINISTRATION FLAG     
     = 0   TAKE ALL NORMAL CYS-CYS BONDS  
     = 1   TAKE ONLY NORMAL CYS-CYS BONDS IN THE SAME CHAIN   
                                          
 124       NUMBER OF CYCLES IN DISTAN/MODFIT REFINEMENT  
 125       NUMBER OF ITERATIONS PER CYCLE IN DISTAN/MODFIT REFINEMENT 
 126       IF MAX SHIFT < 126/1000.0 STOP CYCLE ONE IN DISTAN MODFIT  
 127       IF MAX SHIFT < 126/1000.0 STOP CYCLE OTHER IN DISTAN MODFIT
 128       DESIRED RMS BOND LENGTH IN DISTAN/MODFIT REFINEMENT     
 129       DESIRED RMS ANGLES IN DISTAN/MODFIT REFINEMENT     
                                          
 130-139   PARAMETERS RESERVED FOR THE MAPEDIT MODULE    
                                          
 140-149   PARAMETERS RESERVED FOR THE MDF OPERATIONS    
                                          
 200-220   PARAMETERS RESERVED TO HOLD VAN DER WAALS RADII    
                                          
 221-231   PARAMETERS RESERVED FOR THE EXECUTION OF PROGRAM GRIN    
                                          
 232-250   PARAMETERS RESERVED FOR THE EXECUTION OF PROGRAM GRID    
                                          
 251- 260  PARAMETERS RESERVED FOR MAP OPERATIONS   
                                          
 251       DEFAULT PROPERTY MAP SIZE (=48) 
                                          
 252       FREE SIZE AROUND THE MAP IN ANGSTROMS (=3)    
                                          
 253       CHGMAP FUNCTION SELECTOR (DEFAULT=1)     
                                          
 254       FLAG FOR AUTOMATIC USAGE OF MASMAP OPTIONS    
     = 0   PROMPT USER FOR ALL INPUT PARAMETERS     
     = 1   TAKE DEFAULT OR PRESET PARAMETER FOR EVERY INPUT PARAMETER 
                                          
 255       REMOTENESS VALUE FOR MAS002 (DEFAULT=10) 
                                          
 256       MINIMAL VALUE FOR MAP VALUES UPON SCALING (=0)     
 257       MAXIMAL VALUE FOR MAP VALUES UPON SCALING (=100)   
                                          
 258       NUMBER OF CYCLES IN SMOOTHING (MAS006)   
                                          
 259       NUMBER OF CYCLES IN SHELL (MAS008)  
                                          
 261-269   MALI/PRALI MULTI SEQUENCE ALIGNMENT PARAMETERS.    
                                          
 270       ATOM-TO-USE FLAG FOR GRA1DB    
     = 0   DRAW ALL ATOMS FOR THIS DATABASE AMINO ACID.  
     = 1   DRAW ONLY THE SIDE CHAIN ATOMS FOR THIS DATABASE AMINO ACID
     = 2   DRAW ONLY THE MAIN CHAIN ATOMS FOR THIS DATABASE AMINO ACID
     = 3   DRAW ONLY THE TAGGED ATOMS FOR THIS DATABASE AMINO ACID 
                                          
 271       PART-OF-HIT TO SHOW FLAG FOR SCNGRN HITS 
     = 0   SHOW CENTER PLUS TWO NEIGBOURS 
     = 1   SHOW FULL HIT                  
     = 2   SHOW CENTER PLUS BACKBONE OF FULL HIT    
     = 3   SHOW ONLY ATOMS TO BE USED FOR SUPPOS    
     = 4   SHOW ONLY SIDE CHAIN OF HIT    
                                          
 273       MAKE WHOLE RESIDUE OR JUST C-ALPHAS PICKABLE IN MOVIE   
     = 0   ONLY C-ALPHAS                  
     = 1   WHOLE RESIDUES                 
                                          
 272       COLOUR DATABASE HIT FLAGS      
     = 0   USE UNIFORM COLOUR             
     = 1   USE INDIVIDUAL ATOMIC COLOURS  
                                          
 274       NUMBER OF PICKABLE DATABASE HIT ATOMS (NOT USER SETTABLE)  
                                          
 275       COLOURING SCHEME FOR DATABASE HITS  
     = 0   COLOUR BY POSITION IN THE HIT LIST  
     = 1   COLOUR BY FIT QUALITY          
     = 2   COLOUR BY ATOM TYPE            
     = 3   COLOUR BY B-FACTOR             
     = 4   COLOUR BY ACCESSIBILITY        
                                          
 276       NUMBER OF ENTRIES FOUND IN THE TOPOLOGY FILE  
                                          
 277       SKIP DNA/RNA UPON READING PDB FILE FLAG  
     = 0   DO NOT SKIP DNA/RNA            
     = 1   SKIP DNA/RNA                   
                                          
 278       USE ORIGINAL OR WHAT IF HST DETERMINATIONS    
     = 0   CONVERT DSSP HST DETERMINATIONS INTO WHAT IF NOMENCLATURE  
     = 1   MAINTAIN THE ORIGINAL DSSP NOMENCLATURE  
                                          
 279       ARE WE IN PDB-CHECK MODUS?     
     =-1   WE WANT NO CHECK OUTPUT WHATSOEVER  
     = 0   NO, WE ARE IN NORMAL MODUS     
     = 1   YES WE ARE IN CHECK MODUS      
                                          
 280 - 289 PARAMETERS RESERVED FOR QUALITY BOXES    
                                          
 280       LEVEL OF OUTPUT FLAG IN QUALITY CONTROL  
     = 0   ONLY SHOW INFORMATION AT A RESIDUE LEVEL 
     = 1   SHOW INFORMATION ABOUT RESIDUE AND ATOM LEVEL 
     = 2   SHOW INFORMATION AT DEBUG LEVEL     
                                          
 281       FLAG TO DETERMINE HOW TO EVALUATE QUALITY CONTROL VALUES   
     = 0   TAKE NEAREST POINT IN QUALITY CONTROL BOX     
     = 1   CONVOLUTE WITH THE CONTROL BOX WITH AN ATOMIC VOLUME    
                                          
 282       VAN DER WAALS RADIUS OF ATOMS UPON CREATION OF QUALITY  
           CONTROL BOXES. DEFAULT=1.8 (*100.0) 
                                          
 283       VAN DER WAALS RADIUS OF ATOM UPON CONVOLUTING ATOMIC SPACE 
           WITH QUALITY CONTROL BOX. DEFAULT=1.8 (*100.0)     
                                          
 284       FLAG TO SKIP BACKBONE OF NEIGBOUR RESIDUES    
     = 0   DON'T SKIP ANY ATOM AT ALL.    
     = 1   SKIP MAIN CHAIN ATOMS OF COVALENT NEIGHBOUR RESIDUES    
                                          
 285       FLAG TO DETERMINE CONTACT VALUATION MODE 
     = 0   USE WHOLE NEIGHBOUR IN CASE OF CONTACT   
     = 1   USE ONLY CONTACTING ATOM       
                                          
 286       FLAG TO DETERMINE IF CB WILL BE SHOWN IN BB OPTION 
     = 0   DO SHOW CB (IF NOT GLY)        
     = 1   DO NOT SHOW CB                 
                                          
 298       FLAG FOR WRITING ACCESSIBILITIES IN PDB FILE OR NOT     
     = 0   DO NOT WRITE ACCESSIBILITIES   
     = 1   DO WRITE ACCESSIBILITIES       
                                          
 300 - 370 RESERVED FOR GROMOS AND PRE-GROMOS. 
                                          
 300       LEVEL OF USAGE FLAG.           
     = 0   CREATE INPUT/JOB FILES, DO NOT EDIT THEM, RUN JOB    
     = 1   CREATE INPUT/JOB FILES, EDIT INPUT, RUN JOB (DEFAULT)    
     = 2   CREATE INPUT/JOB FILES, EDIT INPUT/JOB, RUN JOB.   
                                          
 301       BATCH FLAG                     
     = 0   RUN EVERY JOB INTERACTIVELY    
     = 1   SUBMIT EVERY JOB TO BATCH      
                                          
 302       WATER FLAG                     
     = 0   RUN IN VACUUM                  
     = 1   USE CRYSTAL WATERS IF AVAILABLE (DEFAULT)     
     = 2   RUN IN WATER BOX RECTANGULAR   
     = 3   RUN IN WATER BOX MONOCLINIC    
     = 4   RUN IN WATER BOX OCTAHEDRAL    
                                          
 303       DID WE ACTUALLY USE WATER?     
     = 0   NO X-RAY WATER WAS FOUND/USED/GENERATED  
     > 0   NUMBER OF X-RAY WATERS INCLUDED (DAANTJE$)    
                                          
 304       NUMBER OF SELECTED DRUG MOLECULES   
                                          
 305       NUMBER OF ATOMS TO BE WRITTEN IN COORDINATE FILE   
                                          
 306       BETA, ANGLE IN GROMOS MONOCLINIC BOX (*100.0) (DAANTJE$)   
                                          
 307       NUMBER OF PROTEIN MOLECULES (DAANTJE$)   
                                          
 308       NUMBER OF RESIDUES TO BE WRITTEN IN COORDINATE FILE     
                                          
 309       DO WE HAVE N-TERMINAL PROLINE? 
     = 0   NO                             
     = 1   YES                            
                                          
 310       ENERGY MINIMIZATION METHOD     
     = 1   STEEPEST DESCENT               
     = 2   CONJUGATE GRADIENT             
                                          
 311       NUMBER OF ENERGY MINIMIZATION STEPS 
                                          
 312       STEPS PER GRADIENT CALCULATION (IN CONJUGATE GRADIENT   
           MINIMIZATION).                 
                                          
 313       SHAKE FLAG                     
     = 0   DO NOT USE SHAKE (SLOW BUT CERTAIN)   
     = 1   USE SHAKE (DAANTJE$: ON ALL BONDS?????)  
                                          
                                          
 314       MINIMAL ENERGY DIFFERENCE BETWEEN TO EM STEPS (*100.0)  
                                          
 315       STEP SIZE IN CASE OF STEEPEST DESCENT (*100.0) 
                                          
 316       MAXIMAL STEP SIZE IN CASE OF STEEPEST DESCENT (*100.0)   
                                          
 317       PAIR LIST CUTOFF DISTANCE IN NANOMETERS (*100.0)    
                                          
 318       CUTOFF FOR LONG RANGE COULOMB INTERACTION IN NANOMETERS 
           (*100.0)                       
                                          
 319       TEMPERATURE DURING MD RUN IN DEGREES KELVIN   
                                          
 320       MAXIMAL ALLOWED ERROR IN TEMPERATURE DURING MD RUN 
                                          
 321       TOTAL NUMBERS OF ATOMS IN WRETWOGRO*.DAT JUST BEFORE MD 
                                          
 322       NUMBER OF PICOSECONDS IN A CONTINUATION MD RUN   
                                          
 323       NUMBER OF SOLUTE ATOMS AFTER PROGCH 
                                          
 324       ADDITIONAL BOND-CHECK IN GRA1AA, ETC.    
     = 0   DON'T CHECK BOND DISTANCES     
     = 1   DO CHECK ADDITIONAL BOND DISTANCES  
                                          
 325       PRESSURE FLAG FOR BOXED MD RUNS     
     = 0   NOT CONSTANT PRESSURE (DEFAULT)     
     = 1   CONSTANT PRESSURE              
                                          
 326       DISTANCE RESTRAINTS FLAG       
                                          
 327       FLAG FOR FASTMD
     = 0   ALL SUBROUTINES WORK NORMAL
     = 1   ALL SUBROUTINES WORK FAST, NO QUESTIONS ARE ASKED                               
                                          
 328       NUMBER OF DRUGS NOT DESCRIBED IN GROMOS FILES 
                                          
 329       NUMBER OF PICOSECONDS FOR HEATUP/WRUNMD  (HTSTEP)    
                                          
 331       FIX ALPHA CARBONS FLAG         
     = 0   DO NOT FIX ALPHA CARBONS IN EM AND MD    
     = 1   DO FIX ALPHA CARBONS IN EM AND MD   
                                          
 332       FORCE CONSTANT FOR ALPHA CARBON FIXING   
                                          
 333 = 0   DO NOT USE STOUTEN-SANDER SOLVATION TERM 
     = 1   USE STOUTEN-SANDER SOLVATION TERM   
                                          
 334 = 0   USE MD (DEFAULT)               
     = 1   USE SD                         
                                          
 335       SELECT FLAG FOR WEDTRA         
     = 0   USE ALL ATOMS                  
     = 1   USE CA ONLY                    
     = 2   USE CA + GEOMETRICAL CENTER OF SIDE CHAIN     
     = 3   USE CA + TERMINAL ATOM OF SIDE CHAIN     
     = 4   DIHEDRAL SPACE                 
                                          
 336       PRINT FLAG IN ESSENTIAL DYNAMICS/WAD*  
     = 0   DON'T PRINT PLOTS              
     = 1   PRINT PLOTS                    
                                          
 337       SELECTION OF TRANSLATIONAL FIT TYPE 
     = 0   GC                             
     = 1   CM                             
                                          
 338       SELECTION OF ROTATIONAL FIT    
     = 0   FIT ON SELECTED ATOMS          
     = 1   FIT ON CA PROTEIN              
     = 2   FIT ON ALL ATOMS PROTEIN       
     = 3   FIT ON CA SELECTED PART PROTEIN     
     = 4   FIT ON ALL ATOMS SELECTED PART PROTEIN   
                                          
 339       PLACEMENT OF HYDROGENS IN GROMOS 
     = 0   OLD FASHIONED PROGCH                             
     = 1   SLOW BUT ADVANCED RWWH METHOD                             
                                          
 340       WRITE TRAJECTORIES TO A FILE OR NOT FLAG 
     = 0   DO NOT WRITE TRAJECTORIES      
     = 1   DO WRITE OUT TRAJECTORIES      
                                          
 341       NUMBER OF STEPS AFTER WHICH A TRAJECTORY IS WRITTEN     
                                          
 342       NUMBER OF POSITIVE IONS IN WATER BOX     
                                          
 343       NUMBER OF NEGATIVE IONS IN WATER BOX   

 344       FLAG WHICH DETERMINES HOW AN MDRUN SHOULD BE INITIATED
     = 0   USE WRUNMD
     = 1   USE HEATUP  
                                          
 345       LOWEST NUMBER OF RANGE ON WHICH EPAA RAN 
                                          
 346       HIGHEST NUMBER OF RANGE ON WHICH EPAA RAN     
                                          
 347       NUMBER OF WATER MOLECULES ADDED IN PROBOX (?) 
                                          
 348       CELL DIMENSION OF WATER BOX IN X DIRECTION * 100000     
                                          
 349       CELL DIMENSION OF WATER BOX IN Y DIRECTION * 100000     
                                          
 350       CELL DIMENSION OF WATER BOX IN Z DIRECTION * 100000     
                                          
 351       FLAG WHICH DETERMINES HOW ATOMS ARE SELECTED IN WADTRA
     = 0   USE STANDARD TTY INTERFACE
     = 1   USE GRAPHICS PICKING  

 352       PROJECT NUMBER                 
                                          
 355       GRID STEPS IN ANAVOL OPTION (DEFAULT=50) 
                                          
 356       GRID SPACING IN ANAVOL OPTION (*100) (DEFAULT=.25) 

 360       NUMBER OF ATOMS IN THE TRAJECTORY PRODUCED BY WADINI

 361       NUMBER OF FRAMES IN THE TRAJECTORY PRODUCED BY WADINI
                                          
 371       GAP OPEN PENALTY IN WALIGN     
                                          
 372       GAP ELONGATION PENALTY IN WALIGN    
                                          
 373       GAP OPEN PENALTY IN ALIPRF     
                                          
 374       GAP ELONGATION PENALTY IN ALIPRF    
                                          
 401 - 410 RESERVED FOR WATER MENU        
                                          
 401       DISTANCE OF WATER TO RESIDUE IN ORDER TO BELONG WITH IT 
                                          
 402       WATER NUMNAM BIAS (ADDED TO EVERY SEQUENTIAL WATER NUMBER) 
                                          
 403       FLAG FOR WATER USAGE IN SCREEN MENU ITEM NAYB 
     = 0   SHOW CONTACTS FROM RESIDUES TO NEIGHBOUR RESIDUES AND WATERS----
           AND FROM PICKED WATERS TO RESIDUES AND ENVIRONMENT WATERS  
     = 1   SHOW ONLY RESIDUE-RESIDUE CONTACTS  
     = 2   SHOW ONLY WATER WATER CONTACTS 
                                          
 411 - 420 RESERVED FOR MASMAP MENU       
                                          
 412       DIFFERENCE IN SPIKER OPTION (MAS018)     
                                          
 413       ATTENUATION IN SPIKER OPTION (MAS018)    
                                          
 414       TRUNCATION LEVEL AND NEW VALUE IN FLATEN OPTION (MAS013)   
                                          
 421 - 430 RESERVED FOR THE AUTO SUPPOS OPTION 
                                          
 421       SEQUENCE OR PACKING FLAG       
     = 0   USE ALL RESIDUES IN SUPPOS REFINEMENT LOOPING 
     > 0   USE ONLY STRETCHES OF THE INDICATED LENGTH    
                                          
 422       SUPPOS CALLED FROM SPCIAL MENU FLAG 
     = 0   DEFAULT. SUPPOS IS USED NORMALLY    
     = 1   SUPPOS IS CALLED FROM SPCIAL TO MAKE 3SSP FILES  
 
 431       Lower residue of horizontal contact range  
                                          
 432       Higher residue of horizontal contact range  
                                          
 433       Lower residue of vertical contact range  
                                          
 434       Higher residue of vertical contact range  
                                          
 441 - 460 RESERVED FOR DNA REGULARIZATION OPTION   
                                          
 441       WEIGHT FACTOR ON BOND LENGTHS (*100)     
                                          
 442       WEIGHT FACTOR ON BOND ANGLES (*100) 
                                          
 443       WEIGHT FACTOR ON TORSION ANGLES (*100)   
                                          
 444       WEIGHT FACTOR ON PLANARITIES (*100) 
                                          
 445       OVERALL TRANSLATIONAL DAMPING FACTOR (*100)   
                                          
 461 - 480 RESERVED FOR GENERAL OPTIONS   
                                          
 461       USE OWN MOLECULE IN ACCESSIBILITY CALCULATIONS OR NOT   
     = 0   DO USE THEM                    
     = 1   DO NOT USE THEM                
                                          
 481 - 490 RESERVED FOR HYDROGEN BONDS    
                                          
 481       MAXIMAL ALLOWED DONOR ACCEPTOR DISTANCE (3.5A) *100     
                                          
 482       VALUE OF WIFPAR(56) AT MOMENT NEIGHBOUR TABLE IS BEING MADE
           THIS PARAMETER IS NEEDED TO MAKE SURE THAT THE NEIGHBOUR 
           TABLE CORRESPONDS WITH THE H-BOND DISTANCE   
                                          
 483       NEIGHBOUR TABLE HETEROGENEITY FLAG  
     = 0   HOMOGENEOUS                    
     = 1   HETEROGENEOUS (NEIGHBOUR TABLE NEEDS RECALCULATION)     
                                          
 484       MAXIMAL HYDROGEN ACCEPTOR DISTANCE (2.5A) *100     
                                          
 485       MAXIMAL ANGULAR ERROR OVER HYDROGEN (60) 
                                          
 486       MAXIMAL ANGULAR ERROR OVER ACCEPTOR (90) 
                                          
 487       H-BOND GRAPHICS FLAG           
     = 0   ERROR                          
     = 1   SHOW HBONDS AT TERMINAL, BUT NOT AT PS300     
     = 2   SHOW HBONDS AS DONOR ACCEPTOR DOTTED LINES    
     = 3   SHOW HYDROGENS AND HBONDS      
                                          
 488       HBONDS DEBUG FLAG              
                                          
 489       USED.                          
                                          
 491       PRESENT SOUNAM POINTER         
                                          
 492       ANGULAR SPREAD IN CONNOLLY'S TRB CALCULATION (*100) 
                                          
 494       PROBE RADIUS IN CONNOLLY'S PROGRAM (*100)     
                                          
 500-520   PARAMETERS FOR THE NEURAL NETWORK MODULE 
                                          
 501       NUMBER OF INPUT NODES (DEFAULT=3)   
                                          
 502       WIDTH OF THE HIDDEN LAYERS (DEFAULT=5)   
                                          
 503       NUMBER OF HIDDEN LAYERS (DEFAULT=3) 
                                          
 504       SOFT LIMIT FOR NEURON VALUES (DEFAULT=2) 
                                          
 505       HARD LIMIT FOR NEURON VALUES (DEFAULT=5) 
                                          
 506       MAXIMAL STEP SIZE*100 (DEFAULT=100*2.0)  
                                          
 507       WRITE TEACHING SET ECHO IN NEURAL TRAINING(1) OR NOT(0) 
                                          
 508       NUMBER OF PRESENT NEURAL NETWORK SAVE FILE    
                                          
 524       GROUP NUMBER FOR OPTIONS THAT USE GROUPS WITHOUT USER IO   
                                          
 525       SAVE-FILE NUMBER FOR SAVSOU AND RESSOU OPTIONS     
                                          
 531       LINE WIDTH FOR GRAPHICS         
                                          
 532       FLAG TO TELL WIF425 ETC. THAT WE HAVE A CA-ONLY RESIDUE 
                                          
 535       ENTRY POINT IN ADD MENU OF PERSONAL MENU 
                                          
 536       OBJECT NUMBER TO OVERRULE GRAMOLS QUESTIONS   
                                          
 537       NUMBER OF LAST CREATED OBJECT  
                                          
 538       DEBUG FLAG TO TRACE CENTERING PROBLEMS   
                                          
 539       HELIX TYPE FLAG IN DAVID THOMAS' RIBBON OPTION     
     = 0   DEFAULT HELICAL CYLINDERS      
     = 1   SPIRAL HELICES                 
                                          
 540       NUMBER OF THREADS PER HALF ARROW (DEFAULT=5)  
                                          
 541       HELICAL CURVE WEIGHT (1.0=1000)     
                                          
 542       HELICAL SLOPE WEIGHT (0)       
                                          
 543       STRAND CURVE WEIGHT (1.0=1000) 
                                          
 544       STRAND SLOPE WEIGHT (0)        
                                          
 545       LOOP CURVE WEIGHT (0.001=1)    
                                          
 546       LOOP SLOPE WEIGHT (0.001=1)    
                                          
 547       LOOPS AS SPLINE OR CA-TRACE    
     = 0   SPLINE                         
     = 1   CA-TRACE                       
                                          
 548       CYLINDERS BLUNT OR ARROWED     
     = 0   BLUNT                          
     = 1   ARROW HEADED                   
                                          
 549       STRAND ROUTINE IS CALLED IN AUTOMATIC MODE    
     = 0   MANUAL MODE (DEFAULT)          
     = 1   AUTOMATIC MODE (DO NOT PLOT, KEEP VECTORS) 
                                          
 550       MULTIPLICATIVE FACTOR ON STRAND WIDTH (*100.0)     
                                          
 551       NUMBER OF THREADS IN A SPIRAL HELIX (DEF=2*3+1)    
                                          
 552       SCALEFACTOR FOR POSTSCRIPT OUTPUT   
                                          
 553       X-BIAS FOR POSTSCRIPT OUTPUT   
                                          
 554       Y-BIAS FOR POSTSCRIPT OUTPUT   
                                          
 555       WRITE PLOT PARAMETERS OR NOT FLAG   
     = 0   DEFAULT, DO WRITE THEM         
     = 1   DO NOT WRITE PLOT PARAMS, AS WE ARE IN MULTI PLOT MODE. 
                                          
 556       USE ACCESSIBILITY IN DGLOOP FLAG    
     = 0   DEFAULT, DO NOT USE ACCESSIBILITY.  
     = 1   USE ACCESSIBILITY.             
                                          
 557       LOWER LIMIT OF ACCESSIBILITY IN DGLOOP (0)    
                                          
 558       UPPER LIMIT OF ACCESSIBILITY IN DGLOOP (1000) 
                                          
 559       MAXIMAL NUMBER OF ALLOWED RELAX STEPS IN DG OPTIONS (1) 
                                          
 560       CONTINUOUS SHOSOU FLAG         
     = 0   OPTION DE-ACTIVATED            
     = 1   DO NOT UPDATE IN IRI000        
     = 2   NEXT PASS THROUGH IRI000, UPDATE CONTINUOUS SHOSOU 
                                          
 561       INTEGRATED QUALITY CONTROL SCORE OVER RANGE   
                                          
 562       USE WIFGRN IN QUA028 FLAG      
     = 0   DO NOT LOOK AT WIFGRN IN QUA028  
     = 1   ONLY USE RESIDUES FOR WHICH WIFGRN=.TRUE. IN QUA028     
                                          
 563       NUMBER OF CORRECTIONS MADE BY LAST CALL TO GRO010  
                                          
 564       NUMBER OF RELAX STEPS ALLOWED IN DGLOOP OPTIONS    
                                          
 565       AUTOMATIC MODE IN WALIGN (OPTION HIDE08) FLAG 
     = 0   WE ARE IN MANUAL MODE          
     = 1   WE ARE IN AUTOMATIC MODE       
                                          
 566       FILLED PLOT MODE IN STRAND OPTION   
     = 0   WE ARE IN NORMAL MODE          
     = 1   WE ARE IN FILLED PST MODE      
                                          
 567       DEPTH QUEUEING ON IN PSTPLT?   
     = 0   WE ARE IN NORMAL MODE          
     = 1   WE ARE IN DEPTH QUEUEING PST MODE   
                                          
 568       NUMBER OF NAYB RESIDUE          
                                          
 569       RESTRICTED ROTATION FLAG       
     = 0   WE ARE IN NORMAL MODE          
     = 1   ROTATE AROUND X ONLY           
     = 2   ROTATE AROUND Y ONLY           
                                          
 570       NUMBER OF COMPLICATED FOLLOW ME SPHERE CENTRAL RESIDUE  
                                          
 571       Backup of 570 in case SPHR is toggled off     
                                          
 572-576   Toggle switches for continuous update tables at screen  
                                          
 577       Number of sequences for which there is a CMCODE    

 578       Number of NAYB atom
                                          
 581-584   PHI/PSI OF IAA-1/IAA+1 FOR DGLOOP PURPOSES    
                                          
 585       IAA ON WHICH DGLOOP WORKS AT THE MOMENT  
                                          
 586       DO WE HAVE RESIDUES IN THE SOUP     
     = 0   YES THERE ARE RESIDUES         
     = 1   THERE ARE PERHAPS NO RESIDUES IN THE SOUP     
                                          
 587       DO WE USE THE RUBBER BANDING OPTION 
     = 0   NO WE DO NOT USE RUBBERS         
     = 1   YES WE ARE USING RUBBERS       
                                          
 588       FIRST RESIDUE IN RUBBER BANDING MOLECULE 
                                          
 589       LAST RESIDUE IN RUBBER BANDING MOLECULE  
                                          
           590 - 600 RESERVED FOR ROB HOOFT         
 590       "USESYM": 1 = Use symmetry in options that can     
 591       "PCKSYM": 1 = Pick symmetry related atoms     
 592       "LCKSYM": 1 = Lock symmetry matrices. no changes allowed   
 593       Default maximum number of entries in a PDBOUT table     
 594       Are we multiplying H-bond potentials with a B-factor comp? 
     = 0   NO WE ARE NOT                  
     = 1   YES WE ARE                     
 595       Are we ignoring hydrogen bonds between water molecules? 
     = 0   NO WE ARE NOT                  
     = 1   YES WE ARE                     
 596       The number of HB2MCX runs to perform for an optimization   
                                          
 601       ARE WE RUNNING DGINS AT THE MOMENT  
     = 0   NO WE ARE NOT                  
     = 1   YES WE ARE                     
                                          
 602       ARE WE USING HBONDS IN DEBUMP AT THE MOMENT   
     = 0   NO WE ARE NOT                  
     = 1   YES WE ARE                     
                                          
 603       ARE WE SKIPPING BUMPS IN DGLOOP     
     = 0   NO WE ARE NOT                  
     = 1   YES WE ARE                     
                                          
 604       NUMBER OF THE RESIDUE BEING DGLOOP-ED    
                                          
 605       ARE WE USING AMBER TRAJECTORIES     
     = 0   NO WE ARE NOT                  
     = 1   YES WE ARE                     
                                          
 606       DEBUMP AGAINST THE FULL SOUP   
     = 0   NO WE ARE NOT                  
     = 1   YES WE ARE                     
                                          
 607       DO WE WANT IMPORTANCE UPDATES DURING MODELING 
     = 0   NO WE DO NOT                     
     = 1   YES WE DO                      
                                          
 608       DO WE WANT TO ALWAYS MODEL LYS/MET DURING MODELING 
     = 0   NO WE DO NOT                     
     = 1   YES WE DO                      
                                          
 609       DO WE WANT TO SUPPRESS OUTPUT DURING MODELING 
     = 0   NO WE DO NOT                     
     = 1   YES WE DO                      
                                          
 610       FIRST NUMBER AT END OF TRAJECTORY   
                                          
 611       SECOND NUMBER AT END OF TRAJECTORY  
                                          
 612       THIRD NUMBER AT END OF TRAJECTORY   
                                          
 613       USE CELL PARAMETERS OF TRAJECTORY FOR COLOURING?   
     = 0   NO WE DO NOT                     
     = 1   YES WE DO                      
                                          
 614       NUMBER OF MOL-OBJECT 1 FOR TOGGLING 
                                          
 615       NUMBER OF MOL-OBJECT 2 FOR TOGGLING 
                                          
 616       NUMBER OF STEPS DONE FOR TOGGLING   
                                          
 617       NUMBER OF STEPS PER STEP FOR TOGGLING    
                                          
 618       USE BENT HELICES IN SPLINE OPTION   
     = 0   YES WE DO                      
     = 1   NO WE DO NOT                     
                                          
 619       COLOUR OF PICK LABEL (0 MEANS USE DEFAULT)    
                                          
 620       NUMBER OF VECTORS IN MOVING MOL-ITEM     
                                          
 621       CRIPPLE MODE FOR TUTORIALS      
     = 0   NO WE ARE NOT CRIPPLE           
     = 1   YES WE ARE CRIPPLE              
                                          
 622       DELETE OVERLAPPING RESIDUES    
     = 0   YES, AUTOMATICALLY             
     = 1   YES, BUT AFTER A QUESTION      
     = 2   NO, HANDS OFF, KEEP THEM       
                                          
 623       NUMBER OF RESIDUE PRESENTLY BEING HAND-CHECKED     
                                          
 624       SHOULD NOMENCLATURE ERRORS BE WRITTEN IN CHECK SUMMARY  
     = 0   NO                             
     = 1   YES                            
                                          
 701       SIMPLE MODE FLAG FOR QUICK LOOKING  
     = 0   NO WE DO NOT                     
     = 1   YES WE DO                      
                                          
 702       SIMPLE MODE SPACE FLAG         
     = 0   YES THERE WERE EMPTY OBJECT(S) 
     = 1   NO THERE WERE NO EMPTY OBJECT(S)    
                                          
 703       RUN GRO010 FLAG                
     = 0   YES ALWAYS RUN IT              
     = 1   NO SKIP IT WHEN CALLED         
                                          
 704       NUMBER OF TIMES WIF104 SHOULD SKIP OUTPUT     
                                          
 705       DID OPTION PRODUCE OUTPUT?     
     = 0   NO                             
     = 1   YES                            
                                          
 706       MINIMAL SEQUENCE IDENTITY IN GENPRF 
                                          
 707       MINIMAL PROFILE CONVOLUTION IN GENPRF    
                                          
 708       LENGTH OF ARRAYS IN WIF426     
                                          
 709       IS WIFGRN CALLED FROM WIFWTF (IN OTHER WORDS, SHOULD WIFGRN
           REPEAT QUESTION AFTER ERROR)?  
     = 0   NO                             
     = 1   YES                            
                                          
                                          
 710       SHOULD IRI_002 LOOP OR RETURN  
     = 0   LOOP                           
     = 1   RETURN                         
                                          
                                          
 711       INTERNAL HIDDEN RETURN VALUE: LAST HB2 HYDROGEN BOND VAL   
                                          
 712       ARE WE RETRIEVING IN/OUTPUT VIA TCL?     
     = 0   NO                             
     = 1   YES                            
                                          
 713       LOWER RESIDUE OF STRUCTURE RANGE IN HOMOLOGY MODELING  
                                          
 714       HIGHER RESIDUE OF STRUCTURE RANGE IN HOMOLOGY MODELING 
                                          
 715       WARP FACTOR FOR DEMO           
                                          
 716       Desired luminance of non-black colors

 717       Expected luminance of red

 718       Expected luminance of green

 719       Expected luminance of blue

 801       MINIMAL SEQUENCE LENGTH IN BIGFILE  
                                          
 802       MINIMAL GUARANTEED OK SEQUENCE LENGTH IN BIGFILE   
                                          
 803       THE LAST FILE GOT OPENED FORMATTED  
     = 0   YES                            
     = 1   NO, UNFORMATTED                
                                          
 804       100*THE UPAPRF GAP UPDATE VALUE     

 805       Colour number of the background on SG machines   

 806       If not zero, use BSEQ always. 

 807       Number of zero-able points into caves.
 
 808       100 * Cavity map resolution.

 809       Type of file read by MOL003B,C,..
     = 0   PDB (default)
     = 1   GROMOS

 810       Debug flag for output in TOPOLOGY file reading
     = 0   give no output
     = 1   give debug output

 811       Lower cololour of range to shift out
 
 812       Upper colour of range to shift out

 813       Atom number in Nardy's special option

 814       Use C-alphas or just 1 residue in suppos in SCNGRL
     = 0   Use C-alphas
     <>0   Use one residue (the WIFPAR(814)-th one)
 
 815       Give debug output is HST_TAB
     = 0   give no output
     = 1   give debug output

 816       Draw balls in ball-and-stick in SPL options
     = 0   draw the balls
     = 1   dont draw the balls

 820       Residue number of drug to be docked

 821       Number of most central atom in drug to be docked

 822       Type of 'force field' used in docking

 823       Flag for interactive force-field convolution in FBRT

 824       Colour of H-bonds in GRAEXT SPL*** options

 825       Use old or new quality control
     = 0   Old
     = 1   New

 826       Read also drugs and waters from database
     = 0   no, don`t read them
     = 1   yes, do read them