colorbyb

NAME

     colorbyB - prepare a vu file from a PDB file colored  by  B-
     value

USAGE

     colorbyB pdbfile xfit.vu -n[ormalize]

DESCRIPTION

     The input pdb file is converted to colored lines  using  the
     same  routines  as in xfit except that the lines are colored
     by Bvalue. If the -normalize flag is  present  then  the  B-
     values are normalized before coloring. This is highly recom-
     mended for comparison purposes as it scales out  any  effect
     of  the  overall B. Unnormalized Bs are colored in intervals
     of 5 on B-value from cool to hot with  the  following  color
     scheme:

                     0 -  5        cyan
                     5 - 10        blue
                    10 - 15        orchid
                    15 - 20        pink
                    20 - 25        red
                    25 - 30        gold
                    30 - 50        yellow
                    >50            white

     Normalized Bs are colored based on the sigma deviation  from
     the mean using the following color scheme:

                    < -2.0         cyan
                    -2.0 - -1.0    blue
                    -1.0 - -0.5    orchid
                    -0.5 -  0.0    pink
                     0.0 -  0.5    red
                     0.5 -  1.0    gold
                     1.0 -  2.0    yellow
                    >  2.0         white

     The B-value coloring can be very useful for comparing  muta-
     tions  with  the native structure. This same coloring can be
     done in xfit under View.

VERSION

     Release 3.2 of XtalView

SEE ALSO

     xtalview(1), xfit(1)