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 14-6-1997 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 database file indicated to work with
5 Output in DEBUMP flag
= 0 Do not give output (unless other flag says to do so)
= 1 Do always give output
= 2 Only give final output per residue
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 Display protons in graphics options
= 0 Yes, display them if possible (Default)
= 1 No, never display them
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 Use sequence information for 2 residues in DGINSS
= 0 Use only for 1 residue
= 1 Use it for two residues
20 Width of the stick of an arrow in Angstroms (*100)
Default=0.5
21 Length of the stick of an arrow in Angstroms (*100)
Default=2.5
22 Width of the point of an arrow in Angstroms (*100)
Default=0.5
23 Length of the point of an arrow in Angstroms (*100)
Default=1.0
24 Number of sides of an arrow
Default=6
25 Colour of an arrow
Default=170
26 Use nearest neighbour in BUMPS and CONTAC runs
= 0 Use them
= 1 Dont use them (deauflt)
27 Graphics flag in BUMPS and CONTAC runs
= 0 Do not show dashed lines for contacts and bumps
<> 0 Show dashed lines for contacts and bumps (default)
28 Draw non-hydrogen bonded hydrogens in HB2GRA
= 0 Draw them (deauflt)
= 1 Dont draw them
29 Radius of the water probe. Default = 1.4 A. (*100)
30 Update PRO/GLY backbone in BLDPIR
= 0 Update the backbone coordinates (default)
= 1 Dont update the backbone coordinates
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 plotting purposes
= 0 Use the user requested line type for the whole plot
= 1 Use the internal conversion table from colour to linetype
38 Lowest colour in colour ranges
39 Highest colour in colour ranges
40 Flag to tell MUTATE that 'self' mutations should be done
= 0 Dont self mutate
= 1 Do self mutate (mainly meant to add protons...)
41 Flag to determine how to grow in the BUILD menu
= 0 Default extension (roughly sheetish)
= 1 Use special angles (see below)
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 a 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 atomic distance * 100.0 (5.0)
46 Flag to tell SHOSOU to always give output
= 0 Make output dependent on type_ahead buffer
= 1 Always give output
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 is 4.0 A.
50 Use default when asking for MOL-object
= 0 Use as default the first empty MOL-object
= 1 Don't use a default
51 Length of groups to search for
= 1 Search for single amino acids
= 2 Search for pairs of amino acids
...
52 100 * the maximal allowed error in Calpha position in
DGLOOP fitting.
53 100 * the allowed RMS error in the total fit in DGLOOP
fitting.
54 Number of hits by DGLOOP
55 Number of DGLOOP hits to be searched (default = 80).
56 100 * The Van der Waals radius overlap limit (Default = 0.25 A)
57 Default B-factor when no B-factor is present upon reading
Default value is 12
58
59 Allowed accessible surface for `buried` residue or atom
Default value is 2 squared Angstrom
60 Use only same set name in bump analysis
= 0 Use everything
= 1 Only look for bumps with residues that are in same set
61 Warn for big errors (e.g. > 10.0 sigma) in REFI.
= 0 Warn for these big errors
= 1 Suppress all REFI error warnings but the summary per step
= 2 Suppress all REFI error warnings
62 Write result in DG matrix filling or not
= 0 Yes, write all limits to output
= 1 No, dont write limits, only store them in common
63 Number of the group in a movie under DOS. (See also 66).
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 Number of hits in movie group. (See also 63).
67 Should we return from WHATIF_LOOP
= 0 WHATIF_LOOP runs an infinite loop
= 1 WHATIF_LOOP executes RETURN after next/this command
68 Number of dots on the dots sphere (formerly IQB).
Do not modify: will be set by WIF083. Change WIFPAR(6)
instead.
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 Do we use pull_down menus
= 0 Yes we do
= 1 No we dont
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 Number of sigma steps above which REFI gives output
77 Special flag for SCNGRN in the SCAN3D menu.
= 0 Write MOL-ITEMS always to the graphics
= 1 Do not write MOL-items to the graphics, but to a file
78 Use secondary structure in REFI or not?
= 0 Default. Do not use backbone forces for secondary structure.
= N Use N*default force towards LOCHST given secondary structure.
79 Mode for accessibility calculation
= 0 (Default) give contact surface
= 1 Give accessible surface
81 Minimal length of stretch in auto suppos (default=15)
82 Maximal individual error in auto suppos (default=100*7.0)
83 Maximal RMS error in auto suppos (default=100*4.0)
84 Do we use hydrogens?
= 0 No
= 1 Yes
85 Lowest residue of range that can be picked
86 Highest residue of range that can be picked
87 Write bad atoms in WIF508 or not?
= 0 Yes, write everything
= 1 No, skip ISATOK=FALSE atoms
88 Suppress output during sequence reading
= 0 Print everything
= 1 Suppress output during sequence reading
89 Where do we open WALIGN.BIG
= 0 In the local directory
= 1 On /usr/tmp/
90 Cutoff distance for NAYB option (Default=4.0(*100))
91
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 Force SHAKE to overwrite SHAMAT if new range is narrower
= 0 Never overwrite existing SHAMAT values
= 1 Overwrite SHAMAT if new range is narrower
= 2 Overwrite SHAMAT always
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 Fix-force in REFI
114 Insert extra residue in UPAPRF in more insertions are
seen than this parameter.
115 Refine chain breaks after BLDPIR?
= 0 Dont close gaps (default)
= 1 Close gaps after modelling
116 Last picked point from second pick list
117 Use CAVITY (MAP006) interactively or not
= 0 Use it interactively
= 1 Use defaults everywhere in MAP006
118 Input status after WIFGRN (needed to separate erroneous
input from user input of 0 (zero).
= 0 Input was error free
= 1 Input contained an error
119 Cutoff for cavity in order to be called cavity
120 Only accept second picklist
= 0 Accept all picks
= 1 Accept only second picklist (and menus)
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 REFI
125 Number of iterations per cycle in REFI
126 Prompt for ranges in COLATV
= 0 Prompt for the ranges
<>0 Do NOT prompt for the ranges, but keep what we have
127 Old or new contour lines in Ramachandran plot?
= 0 New contour lines
= 1 Old contour lines
128 Size of GRACHI crosses (*100)
129 Colour of GRACHI crosses
130-137 PARAMETERS RESERVED FOR THE MAPEDIT MODULE
138 Dirty hack for proton klonking
= 0 No dirty hack.
= 1 Tell klonk to dream up empty protons
139 Intended number of sequences per page in pretty plot
140 Intended number of amino acids per line in pretty plot
149 100*scalefactor for characters
150 Number of equivalent residues required for pretty-boxing.
154 If not zero run MOL200 later 'again'
155 Plot file output type
= 0 Postscript
= 1 HPGL
= 2 Robjes stuff to directly write Xfig
156 Lower residue of the SHAKE range
157 Upper residue of the SHAKE range
158 Force structure inversion in the REFI flip routine
= 0 Ask the user if coordinates need hand inversion
= 1 Invert the hand when needed. Dont ask anything.
160 Use sigma in CORMUT or not
= 0 Use sigma in CORMUT
= 1 Dont use sigma in CORMUT
161 Use FLEX in automatic mode or not
= 0 WHAT IF commands are normally asked
= 1 FLEXX is now the boss
162 General FLEX is active flag
= 0 FLEX is not active
= 1 FLEX is active
163 Draw nameless electron density map for FLEX
= 0 Just normally prompt user for map name in WIF152
= 1 Call the map output FLEXMAP in WIF152
164 Z-score on distances in REFI
165 Z-score on angles in REFI
166 Number of some kind of rounds in SHAKE
167 Z-score on chiral volumes in REFI
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 Fixed next MOL-object number for DOS objects
252 Free size around the map in Angstroms (=3)
253 Fixed next MOL-item number for DOS objects
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 ID1 of XTC file in GROMOS applications
260 Print all vectors in GRAMOL
= 0 Dont print
= 1 Print them at the screen
261 Using Amber?
= 0 No we are not going to read Amber stuff.
= 1 Trajectories etc., are Amber stuff.
262 NUMGRO for Amber files
263 Debug flag for GETMOL
264 Refresh counter in IRI000
265 Colour of top identifier bar
266 Colour of top identifier text
267 Initial atom colours. (-1 means colour by atom type).
268 Colour of help text in pop up help boxes.
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 X 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)
330 HACK. TRUE number of MD steps
= 0 Dont use.
<>0 Put instead of number of calculated steps.
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
353 TRAJECTORY FORMAT
= 1 XTC
= 2 ASCII
355 GRID STEPS IN ANAVOL OPTION (DEFAULT=50)
356 GRID SPACING IN ANAVOL OPTION (*100) (DEFAULT=.25)
357 100 * X coordinate of center of molecule
358 100 * Y coordinate of center of molecule
359 100 * Z coordinate of center of molecule
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
380 100*Weight on backbone fit in homology building. RCONFI(1)
381 100*Weight on rotamer density in homology building RCONFI(2)
382 100*Weight on quality control in homology building RCONFI(3)
383 100*Weight on bumps in homology building RCONFI(4)
384 100*Weight on phi-psi misfit in homology modeling RCONFI(5)
385 H-bond MC cutoff RCONFI(6)
386 Aspect ratio on DOS systems RCONFI(7)
387 Initial slab value RCONFI(9)
388 100*Weight on hydrogen bonds in homology building RCONFI(12)
389 Colour map contour lines by atom type
= 0 Colour them as indicated by PARMAP
= 1 Colour them as function of atom type
390 Are we running the tutorial?
= 0 No, we are not
= 1 Yes we are
391 Use the own set or more in contact determinations
= 0 Use everything
= 1 Only use the own set
392 Number of residues to be used in SHAKE superpositions
395 Dont paste in SPC014 (for GETDBF).
= 0 Paste everything
= 1 Dont paste everything.
396 First atom of chiral torsion angle quartet
397 Second atom of chiral torsion angle quartet
398 Third atom of chiral torsion angle quartet
399 Fourth atom of chiral torsion angle quartet
400 Z-score on the chiral torsion angle quartet
401 Distance cutoff in NETWAT option
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
404 Make new water group after water subset determinations?
= 0 Only list results, dont make group.
= 1 List results, and make new group out of listed waters.
405 Reject all output flag
= 0 Normally print all output
= 1 Reject (skip) output
406 Lower residue of flexible range in SHARNG
407 Upper residue of flexible range in SHARNG
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 Number of cycles in SHAKE_SHAKE
490 100 * Allowed maximal error in SHAKE_SHAKE
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
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 use it
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
597 Should there be any terminal output
=0 Normal, yes
=1 Suppress everything in GVSTO6 and GVSTT6
598 Which water molecules count in NQA?
=0 All waters.
=50 Ignore water atoms with population below 0.50 [DEFAULT]
=1000 Ignore water atoms completely.
599 Are we running a check over the database?
This is to notify subroutines that stupid poly-UNK proteins
should be skipped
= 0 NO
= 1 YES
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
630 How to measure distance in WIF689B
= 0 Normal distance (default)
= 1 Distance in X direction only
= 2 Distance in Y direction only
= 3 Distance in Z direction only
631 Colour of toptxt (right top of screen messages).
632 Shift (in pixels) of default X coords of text window.
633 Shift (in pixels) of default Y coords of text window
634 Colour of bottom of screen button text
635 ZFUNCT parameter (operating system dependent)
636 Degrees error in phi and psi allowed in DG* options
637 Colour of the text in the status box
638 Maximal length of groups to be used in DGLOOP options
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)
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
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
720 Maximal number of frames in many trajectory options
721 Number of trajectory steps read already
722 100*Z-score on distances in REFI
723 100*Z-score on bond angles in REFI
790 Colour number of the background on SG machines
791 As 790, but in RGB mode
792 LRGBRA uses GETGDE flag
= 0 Dont use GETGDE in LRGBRA
= 1 Do use GETGDE in LRGBRA
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
806 If not zero, use BSEQ always.
807 Number of zero-able points into caves.
808 Overrules resolution in MAP006 (*100)
= 0 Do not overrule automatic resolution in MAP006
<>0 100 * the resolution to be used in MAP006 (CAVITY etc).
809 Type of file read by MOL003B,C,..
= 0 PDB (default)
= 1 GROMOS
= 2 Kinemage
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 for mutate and modeling
= 0 Old
= 1 New
= 2 None of the above
826 Read also non-peptidic drugs and waters from database
= 0 yes, do read drugs and waters
= 1 no, don`t read drugs and waters
827 Read also symmetry information from database
= 0 no, don`t read symmetry information
= 1 yes, do read symmetry information
828 Used old or new secondary structure determination
= 0 Not (yet) known
= 1 DSSP
= 2 Robs stuff
829 Level of sophistication in REFI
= 0 No, do not debump in REFI
= 1 Use bumps as one term in REFI
= 2 Include hydrophobic contacts
= 3 Include hydrogen bonds
= 4
=5 Include course debumping
830 Atomic sequence distance for usage in DGEOM4
831 50 * the spread between upper and lower distances in DGEOM4
832 Number of generated DG structures
833 Use REFI in DGEOM
= 0 Do not use REFI in DGEOM
= 1 Use REFI in DGEOM
834 Fix user given ranges in GROMOS
= 0 Dont prompt user for fix ranges
= 1 Ask user for ranges to be fixed
835 Flag to tell SW-file reader to fil SERVER.BIG
= 0 Dont write in SERVER.BIG
<>0 This flag is SERVER.BIG record number
836 Number of cycles in RANDOM option (default is 10)
837 Print totals in ANASRF option
= 0 Do not print totals in ANASRF option
= 1 Print totals in ANASRF option
838 Print results in quality control
= 0 Do print results in quality control
= 1 Do not print results in quality control
839 Print ATOM records in MAKMOL
= 0 Do not print ATOM records in MAKMOL
= 1 Do print ATOM records in MAKMOL
840 Minimally required identity percentage for alignment
841 Minimally required profile overlap score for alignment
842 Sigma score (*100) below which REFI stops
843 Are we everywhere below WIFPAR(842) in REFI
= 0 No we are not
= 1 Yes we are
844 Should WIFGRN detect clusters for WIFWTF.
= 0 WIFGRN is not called from WIFWTF
= 1 WIFGRN is called from WIFWTF
845 Is CHOOSE active
= 0 CHOOSE is not active
= 1 CHOOSE is active
846 Counter of MODEL records in input PDB file
847 Read one or all MODELs in NMR structures etc.
=-1 Prompt the user what he/she wants (reading N models)
= 0 Read all models
= 1 Read only the first model
848 Debug statements for type-ahead output flag.
= 0 Dont give type ahead debug output
= 1 Give type ahead debug output
849 Number of lines in a PBM file.
850 Number of points per line in a PBM file.
851-858 Help is active in for MOL-object 850+I in TEACH mode
= 0 No HELP present
= 1 Yes, HELP is present
859 Number of characters used by GVFLFI or GVFLFR
860 Default lower residue of input range
861 Default upper residue of input range
862 Tells WIFGRN it is being called by WIFGRS
863 Lower residue of range wherein input residues should fall
864 Upper residue of range wherein input residues should fall
865 100*ROTANG for stereo
866 100*Ca-Ca distance in DIGIT.F
867 100*WGT for 3D score in DIGIT.F
868 Time in seconds for DEMO10 option
869 Skip .NOT.USEAT atoms in drawat
= 0 just draw everything
= 1 draw only those that have USEAT true
870 What scaore to use in WALIGN related options.
= 0 Use identities only.
= 1 Convolute with the Dayhof matrix.
871 10* percentage sequence identity after alignment
872 10* sequence convolution after alignment
873 Number of times bumps were checked in WIF426
874 Number of times bumps were found in WIF426
875 Give useless output in NQA014
= 0 Yes make the screen dirty
= 1 No, behave intelligently
876 Value of WIFPAR(873) at the previous position
877 Value of WIFPAR(874) at the previous position
878 Use DEBUMP and REFI in BLDPIR
= 0 Use everything
<> 1 The higher, the less regularisation.
880 Error upon GETMOL flag
= 0 GETMOL executed error free
<>0 GETMOL encoutered unsolvable problems
881 Use two ranges in FBRT or not
= 0 Use only one range
<>0 Use two ranges
897 dummy to fudge CVS
898 dummy to fudge CVS
899 dummy to fudge CVS
900-949 reserved for Rob
900 Number of X-Y-Z scale parameters to refine in digit.f
901 Number of residues to refine at the same time in POWELL
902 100*Minimal distance 1-3 Ca-Ca for digit.f
903 Should warnings be printed if the 2D-line isn't seen?
1 = Yes!
0 = No!
904 Should "<RETURN>" on the WHAT IF command line do a
screen update?
1 = Yes!
0 = No!
905 For D2D module: convergence is reached if the relative change
in the E value is less than 1/WIFPAR(905)
906 For D2D module: maximum number of iterations
907 For D2D module: 100*ETA
908 For Bumpcheck: 100*ALLOWED_BUMP. Default is 40, which allows
bumps of 0.40 Angstrom before complaining. Purpose: set to 0.0
when building a model.
909 Usage of HASHTABLE in NQA002
0: Do not use hashtable
-1: Initialize hashtable, then use it
1: Use hashtable
910 Number of NQA002 HASH hits
911 Number of NQA002 HASH misses
912 jack-knife value.
913 jack-knife mode
=0 Skip if MOD(ISEQ,WIFPAR(917)).EQ.WIFPAR(912)
=1 Skip if MOD(ISEQ,WIFPAR(917)).NE.WIFPAR(912)
914 Interrupt mode. What do we do in case of interrupts? (Control C)
=-1 Do not install an interrupt handler at all
=0 Ignore completely
=1 Break current operation
=2 Close WHAT IF conditionally
=3 Close WHAT IF unconditionally?
915 Loop a script over a list of files or the WHAT IF database
=-1 Looping over file of files (unit 70)
=0 Not looping
>0 Current internal database number
916 100*Gamma value for X11 color map generation
917 Jack-knife modulo.
918 Jack-knife which?
1=NQA
2=PDBC62
3=LSCRIP (WIF013)
919 1000*Average RAMA score in WHAT IF database
920 1000*Sigma RAMA score in WHAT IF database
921 1000*Average C12 score in WHAT IF database
922 1000*Sigma C12 score in WHAT IF database
923 Has NQA been used?
0 = "No" or "yes, but we should re-initialize"
1 = "Yes, no initialization is needed"
924 Should NQA024 return separate results for each of the atom types?
0 = no
1 = yes
925 Should INF004 complain if it doesn't find the option?
0 = yes. the user asked for the option
1 = no. It was an automatically generated help call
926 Number of atoms read that were discarded because they
do not belong in this residue type
927 Number of atoms read that were discarded because it is
specified more than once
928 Line width for DIGIT.
929 Should an NQA map be scaled by "reverse accessibility"?
0 = No
>0 = Yes, but the scale should not be higher than WP(929)/100.0
930 Are the NQA datafiles present on the system?
0 = No
1 = Yes
931 Are the old QUA datafiles present on the system?
0 = No
1 = Yes
932 Should plots be created by SCTPRP?
0 = Make plots
1 = Suppress plots
933 HB2 debug level
0 = Normal
>0= More verbose
<0= Less verbose
934 MSDB01: 100*Cutoff radius to be used in polymericity determination
935 MSDB01: Number of contacts per 1000 residues to call it a dimer
936 Should drawings also try to draw in POVRAY file?
=0 NO
>0 Unit number where POVRAY file is attached
937 POVRay cylinder mode used by GRTLIN
1=standard bond
2=bond to hydrogen
3=hydrogen bond
938 Color mode in POVray
=0 Use WHAT IF colors
=1 Use POVray colors
939 MSDB01: 100*weight for the 1-3 contacts in determining cluster.
940 MSDB01: Minimum chain length to consider something a protein
941 100* Resolution of last read PDB file.
942 PdbCheck badness counter
<0 disabled
=0 everything OK
1 one little oops encountered
>1 more than one little oops and/or more than zero big oopses
943 Number of NCS comparisons and plots allowed
944 Server mode: never read from stdin, but wait for kill and
continue by reading SERVER.SCR
945 Restrict MAKMOL output
=0 No
=1 Yes, do not output non-polar hydrogens
950 Debug counter in DGLOOP
951 Debug counter in DGLOOP
952 Debug counter in DGLOOP
953 Debug counter in DGLOOP
954 Debug counter in DGLOOP
955 Debug counter in DGLOOP
956 Debug counter in DGLOOP
957 Debug counter in DGLOOP
958 Debug counter in DGLOOP
959 Debug counter in DGLOOP
960 Debug counter in DGLOOP
961 Debug counter in DGLOOP
962 Debug counter in DGLOOP
963 Debug counter in DGLOOP
964 Debug counter in DGLOOP
965 Debug counter in DGLOOP
966 Debug counter in DGLOOP
967 Debug counter in DGLOOP
968 Debug counter in DGLOOP
969 Debug counter in DGLOOP
970 If not zero, print the DGLOOP killer counters
971 REFI also bad atoms or not
=0 Do not refine bad atoms (bad as in ISATOK=FALSE)
=1 Refine everything in REFI
1001-1400 Reserved for Gert
1001 Energy term to be put in ATTVAL in GETETM
1002 Write all atoms in MAKMOL or only those TRUE in a ROW
=0 Write all atoms
=1 Write only those that are TRUE in a ROW
1003 Parameter to prevent recursion between WIF303 and WIF303X
1004 RMS in SUPOPT option (*100)
1005 REFI should also execute SHAKE
=0 Dont do SHAKE in REFI
=1 Run SHAKE in REFI
1007 Number of 'the best' molecule in NMR ensambles.
1008 100* multiplier for SHAKE shift in REFI
1009 Number of drug atoms in soup at time of KLONKUP
1010 Number of water atoms in soup at time of KLONKUP
1011 Colour of protons (0 means HA + 10)
1012 General debug flag (was ICONFI(12))
1013 Skip CHECK routine in SHAKE module
= 0 Skip the check routine
= 1 Execute the check facility
1014 Debug flag in SHABLD
= 0 No debug output
= 1 Some debug output
= 2 Lots of debug output
1015 Steps to skip (0-99) in WAD options
1016 100* Gap open penalty in new profiles
1017 100* Gap elongation penalty in new profiles
1018 Suppress all kinds of output in GPCMAL
= 0 Give normal output
= 1 Suppress output
1019 Use sequence weights in UPAPRF, etc.
= 0 Do not use them
= 1 Do use sequence weights
1020 Prompt or not is case SAVSOU file will be overwritten
= 0 Ask the user if he/she really wants to overwrite
= 1 Overwrite, no matter what
1021 GPCSEL/GPCSPL sorts sequences into directories or not
= 0 do not sort
= 1 sort sequences over the directories if possible
1029 Robjes param uitgecommenteerd
1030 Number of atoms with missing WEIGHT and BFACT
1031 Predefined colour for Ala
1032 Predefined colour for Cys
1033 Predefined colour for Asp
1034 Predefined colour for Glu
1035 Predefined colour for Phe
1036 Predefined colour for Gly
1037 Predefined colour for His
1038 Predefined colour for Ile
1039 Predefined colour for Lys
1030 Predefined colour for Leu
1041 Predefined colour for Met
1042 Predefined colour for Asn
1043 Predefined colour for Pro
1044 Predefined colour for Gln
1045 Predefined colour for Arg
1046 Predefined colour for Ser
1047 Predefined colour for Thr
1048 Predefined colour for Val
1049 Predefined colour for Trp
1050 Predefined colour for Tyr
1052 Use Daantjes dingetje
1051 -1080 reserved for the other topology entries
(after 1052 has gotten renamed
1053 Print subroutine usage in FULLST
=0 No, dont
=1 Yes, do
1054 100*SAVSOU version number
1055 How to use MUTATE
=0 Ask user
=1 Always use fast mode
=2 Always use slow mode
1056 Fix whole backbone in REFI
=0 Dont FIX anything special
=1 Overrule FIX flag and FIX whole back bone
1057 MAKMOL should write DELPHI file
=0 Write normal PDB file
=1 Write Delphi-style PDB file
1058 Default DELPHI grid size
1059 Default DELPHI grid-fill percentage
1060 How far around atoms should potentials be removed
1061 Remove DelPhi potential from 'impossible' locations
=0 Keep your hands of the DelPhi potential map
=1 'Clean' the map by removal of potential from where nothing can go
1062 Tell MOL200 that atom orders got changed (thus MOL199 needed)
=0 Everything is normal
=1 We need MOL199 once more at the end of MOL200
1063 Pointer into residue backup common block
1064 Echo SCRIPT parameters with SCRIPT>>>> etc.
=0 Yes do
=1 No, dont
1065 Did INF004 get its man?
=0 Yes, HELP was found
=1 No HELP was not (yet) found
1066 Are we rubber banding in FBRT?
=0 No, we are not
=1 Yes, do some EM after every cycle
1067 Number of first residue of RUBBER loop
1068 Number of last residue of RUBBER loop
1069 NUMGRO as read in from last open GROMOS file
1070 OXT correctie was done after CUT or PASTE operation
=0 No correction was done
=1 A correction was requested by the user
1071 Skip OXT corrections
=0 Just do normal OXT corrections
=1 Kip OXT corrections
1072 Accept $ commands?
=0 Yes, normally accept them
=1 No, do not accept $ commands
1073 Use preset WRK1TF in HAS003
=0 No, ask for it or use given range
=1 Use WRK1TF as given by calling subroutine
1074 ANIFLX parameter
=0 Nothing special
=1 We are running ANIFLX, use defaults everywhere for INIFLX
1081 Do we need to update the BOUND_TO administration
=0 No, we dont
<>0 Yes, update it in the next MOL200
1401-1500 Reserved for Buggy Bertje and Dumb Daantje
1401-1450 Reserved for GROMACS
1403 Charge of system after pdb2gmx
1407 LASTAT: Last protein/drug atom
1408 CUTOF1: lower cutoff
1409 CUTOF1: higher cutoff
1410 EMSTPS: EM steps
1411 PRSTPS: PR steps
1412 MDSTPS: MD steps
1413 WRTFRQ: non-xtc output freqency
1414 XTCFRQ: xtc output frequency
1415 DELH2O: delete remote H2O?
1416 BOXDIS: minimum protein-box dist
1417 INTLEV: level of interaction
1418 FIXPAR: what kind of position restraints to use
1419 FIXFRC: restraining force
1420 Gert's GMX escape flag
1421 BOX usage: 0 = no box, 1 = cubic
1422 RESPAR: what kind of distance restraints to use
1501-1800 Reserved for Rob
1501 Less than 0.001*WIFPAR(1501) from axis indicates special position
1502 Flag controlling the workings of FBONDI
=0: Find all bound atoms
>0: Find non-H atoms only
<0: Find H atoms only
1503 Guess whether we have an NMR structure here.
=0: probably X-ray structure
=1: NMR
1504 Soup change counter. Will be incremented by 1 every soup change.
To be used in routines to re-initialize themselves at soup changes.
1505 Should "Q" atoms be considered hydrogen atoms?
=0: yes, as usual
=1: no, not
1506 Are we reading a DNA residue? Automatically set in MOL003B
=0 no, we are reading an RNA residue
=1 yes, we are reading a DNA residue
=-1 yes, we have so far not seen that we will be reading RNA
1507 Is the class of the conventional cell different from the input cell
=0 no, or we haven't checked [yet] (done in RCRYST1)
=1 yes
1508 Should we do SYMICMP to NUMAAF or to NUMAAT?
=0 to NUMAAF, water residues could be too big.
=1 to NUMAAT, water residues are small and close to the protein
1509 100*Minimum "weight" for water atoms to be marked usable by HBO010
1518 Debug parameter for stack-frame corruption in PUSH/POP PPP
1801-2000 Reserved for Jens
1801 Number of standard deviations to include in Electrostatic Map
default=5