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