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.
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