[ addBfactor | alignMinCoverage | alignOldStatWeight | axisLength | clashThreshold | cnWeight | consensusStrength | dcWeight | COLOR.bg | COLOR.distanceAtom | COLOR.label | CONSENSUS_strength | densityCutoff | dielConst | dielConstExtern | drop | fogStart | gapExtension | gapOpen | gpWeights | hbCutoff | lineWidth | listUpdateThreshold | mapSigmaLevel | mapAtomMargin | mcBell | mcJump | mcShake | mcStep | mfWeight | mimelDepth | mimelMolDensity | r_out | r_2out | resLabelShift | rsWeight | selectMinGrad | selectSphereRadius | sfWeight | shininess | ssThreshold | ssWeight | ssearchStep | surfaceTension | tempLocal | temperature | timeLimit | tolGrad | tolFunc | tzWeight | vicinity | vwCutoff | vwExpand | vwExpandDisplay | vwSoftMaxEnergy | waterRadius | wireBondSeparation | xrWeight ]

• make map factor
• make map cell

• Search against the protein domain sequence database: use 0.5 or higher
• Search a multidomain sequence against long multidomain sequences: use 0.1 or lower

• Swissprot has N=89,000 sequences. LogN = 4.95
• Reliable pP = LogN + 3, twilight pP is from LogN + 1. to LogN + 3.

 
 build string "ala ala his his" 
 display 
 axisLength=10. 
 display origin 

 
C = C₀ + (100-C₀)*2*(r-0.5) 

user preference for the background color (overwrites icm.clr preference) E.g.

 COLOR.bg = "grey"
 write system preference

• COLOR.distanceAtom
• COLOR.labelAtom
• COLOR.labelResidue
• COLOR.labelSite
• COLOR.labelVar

COLOR.distanceAtom : default colors of interatomic distances

interatomic distance is shown by a dotted line of this default color. These colors and styles can be changed individually.

COLOR.label... default colors of labels.

• COLOR.labelAtom : atom labels
• COLOR.labelResidue : residue labels
• COLOR.labelSite : site labels
• COLOR.labelVar : variable labels

CONSENSUS_strength

regulates the strength of consensus modifying the CONSENSUS.fraction values. The CONSENSUS table controls the rules of consensus derivation from an alignment . This table may look like this:

 
#>T CONSENSUS 
#>-symbol------fraction----residues--- 
   A           80          A 
   C           90          C 
   D           85          D 
   d           60          ND 
... 
... 

• make map cell command and related operations with the electron density,

 
 mode   9  Right5-Mid                # Move rear clipping plane       

The value of fogStart is saved and restored as a system preference. If its value is negative, the fog is not activated, if the value is a positive number between 0. and 1., ICM sets the fog flag on.

Default (0.3)

gpWeights

the rarray of seven weighting factors for the property grid penalty term in the energy function.

Example:

 gpWeights = Rarray( 7, 1. )  # seven weights of 1. each 

See also:

• set type property # setting atom type contributions
• make map potential "gp" .. # generating up to seven grid maps.
• term "gp"

 
 build string "se nad"  # NAD molecule  
 lineWidth = 3.   
 wireStyle="chemistry" 
 display 

See also: GRAPHICS.grobDotSize , GRAPHICS.grobLineWidth , GRAPHICS.mapLineWidth , IMAGE.lineWidth (3D display), IMAGE.lineWidth2D (chemical tables) PLOT.lineWidth , PLOT.gridLineWidth .

listUpdateThreshold

the real maximal displacement of an atom during local minimization which triggers the recalculation of the interaction lists. This mechanism can be suppressed by setting the l_updateLists variable to no

See also: l_updateLists , minimize .

Default (1.5)

See also: map
Default (1.5)

mapAtomMargin

Margin in Angstroms around selected atoms. The margin is added to the positional boundaries to define a submap index box in the Map ( map_source , as_ ) function.

Default (3.0)

mcBell

average relative size of normally distributed montecarlo step from the center of an ellipsoid surrounding the multidimensional variable restraint zone.
Example:

 
 mcBell = 1.0       # places one standard deviation at the rs border 
 mcBell = 2.0       # distribution is two times broader etc.  

• mimelMolDensity
• electroMethod
• show area

See also:

• mimelDepth
• electroMethod

Some r_2out outputs:

• Align or align : for 2 sequences: percent sequence alignment identity
• Axis( R_12transform ) : helix rise in
• Energy( rs simple ) : rmsd of normalized residue energies
• convert : maximal positional deviation upon conversion

• resLabelStyle
• GRAPHICS.resLabelYShift : the number of leading blanks (shifts the label to the right)

 
 read pdb "1fox" 
 convertObject a_ yes no yes no 
 show energy 
 selectMinGrad=80. 
 show a_//G    
 display 
 display a_//G cpk 

See also: compareMethod
Default (5.0).

 
build string "ASDW" 
GRAPHICS.quality = 15. 
shininess = 100. 
display cpk 

• to find the global minimum successfully one needs a combination of persistence if a chosen place with a good sense of when to stop searching in this place and move along to the next one.
• if the temperature is too high, the acceptance ratio improves (gets higher) and wider sampling becomes easier since more high energy conformations are accepted. The downside of this is the low "persistence" (or "lack of patience") of the search procedure. Instead of spending more time in each conformational vicinity to find the real global minimum, the procedure just tries a couple of sub-optimal conformations and jumps away.
• if the temperature is too low the procedure may not cover the global conformational space of interest.

* tempCycle (need to create a variable with that name) If you want to set a cooling temperature schedule, or even a periodic PCR-like temperature schedule, you can define a new rarray array called tempCycle which contains { tempMax, tempMin, period, phase } . For a simulated annealing schedule, set the period to be twice the value of the mncallsMC parameter. T_curr = 0.5(T₁ + T₂₎ + 0.5 ΔT cos( 2π ( phase + x / period )), x = [0:1]

tempCycle = {10000.,600.,2.,0.}  # the whole period is 2 times longer than the simulation
# it will start from t=10000. finish at about 600. 
montecarlo

 
timeLimit = 2.  # two hours  
montecarlo    # will interrupt the simulation in 2 hours 

See also: tolFunc , mncalls , minNumGrad , l_updateLists , listUpdateThreshold .
Default (0.05).

tolFunc

exit criterion for local minimization by looking at the amplitude of the function value decrease during the last four steps of minimization. Minimization is stopped if the function does not decrease more than the parameter value during the last four steps. The negative value means that this criterion is ignored. All criteria, namely tolGrad, mncalls and tolFunc , are checked simultaneously.

See also: tolGrad , mncalls , minNumGrad , l_updateLists , listUpdateThreshold .
Default (-0.01).

See also: TOOLS.tsWeight , term ts
Default (1.0).

 
 compare a_//ca,c,n  # compare by Cartesian RMSD 
 vicinity = 3.0      # conf. are similar if RMSD< 3 A 
 
 compare v_//phi,psi # compare by angular RMSD 
 vicinity = 40.0     # conf. are similar if aRMSD < 40 deg 

• show energy "sf"
• show [area|volume] skin
• display skin

• show [area|volume] surface
• Xyz( as_ r_distance surface) # sampling points above the surface

display surface
Default (1.4).

vwExpandDisplay

Obsolete. Replaced by GRAPHICS.surfaceProbeRadius . See also: GRAPHICS.surfaceDotDensity, GRAPHICS.surfaceDotSize

vwSoftMaxEnergy

Parameter defining maximal energy value of van der Waals repulsion at r -> 0. for the finite approximation van der Waals function ( vwMethod = "soft" ). This parameter must be greater than 0. kcal/mole.
Note that in the "soft" mode, the electrostatic energy will be automatically buffered to avoid singularities. You will see that the electrostatic term "el" changes upon switching from vwMethod=1 to vwMethod=2 .
Default (7.0).

• show energy "sf"
• show [area|volume] skin
• display skin

• display surface
• show [area|volume] surface