mode general calculation control line

weight term weighting line

initwt initial weighting of terms

finlwt final weighting of terms

mmode conjugate gradient control line

xmode crystallographic refinement controls

xlimit crystallographic limits line

scale crystallographic scale factor lines

maxhkl limits on h,k,l and sinθ/λ

atmzon limits on atoms to shift

reszon limits on residues to shift

dielec dielectric constant

refine initiate the refinement

fc calculate structure factors without refinement

nobdf kill output of new bdf

CEDAR

mode Option Code

refinement modes mod model refinement weights 1-5 set to 1.0

ene energy refinement weights 1-6 set to 1.0

xta crystallographic refinement turned on

ext use externally refined shifts and σ's

weighting scheme uni unit weighting on target atoms

sig weight target atoms by inverse σ

list coordinates nol do not list final atom coordinates

lis list final atom coordinates

weight or1 weight for shift towards target coordinates

initwt2 weight for shift towards target bond lengths

3 weight for shift towards target bond angles

4 weight for shift towards target fixed dihedrals

5 weight for shift towards target flexible dihedrals

6 weight for shifts based on non-bonded interactions

7 weight for chiral angles

8 weight for hydrogen atom target coordinate

9 minimum energy for listing bad energy terms no list

finlwt1 final weight for shift towards target coordinates

2 final weight for shift towards target bond lengths

3 final weight for shift towards target bond angles

4 final weight for shift towards target fixed dihedrals

5 final weight for shift towards target flexible dihedrals

6 final weight for shifts based on non-bonded interactions

7 final weight for chiral angles

mmode1 number of conjugate gradient minimization passes 10

2 estimate of error in total force, blank usually

xmode Code Option

uov do not refine overall U

iso isotropic U refinement only

ani anisotropic U if present, else U

pre input coords stored as previous ones

fca use previous FC as fixed atom contribution

fxe establish and apply previous FC as fixed

atom contribution

fxa apply previously established fixed atom

contribution

ski n use every n^th reflection in calculations

xlimitCode Option

min n min U

max n max U

chg n max change multiplier/divider of U from

previous atom to which it is bonded

uni unit weighting on F's in refinement

sig σ weighting on F's in refinement

dam n damping factor on shifts

sgc n do not use reflection with F < n*σ

sft n max shifts (Å) of atom in refinement

scale1 F relative scale factor

2 index to scale group number 1

maxhkl1-3 max |h|, |k|, |l|

4-5 min and max sinθ/λ

atmzon1 residue name¹ of first residue shifted

2 atom label of first atom shifted

3 residue name¹ of last residue shifted

4 atom label of last atom shifted

1 Residue name structure same as mspair line in PRECED

reszon1 residue name¹ of first residue shifted

2 residue name¹ of last residue shifted

1 Residue name structure same as disulf line in PRECED

dielec1 dielectric constant 1.0

refine1 number of refinement passes with current parameters

fccalculate FC without refinement

nobdfno output bdf