[ base | ball | beta | boundary element | BPMC ]
Use option base to display cartoon representations of the bases on the DNA/RNA ribbons.
In DNA and RNA ribbons, bases can be displayed/colored separately from the ribbon itself (e.g.
color ribbon base a_1/* white ), the default coloring being A-red, C-cyan, G-blue, T or U-gold.
a solid sphere representing an atom in the graphics window. Its size is
defined by the GRAPHICS.ballRadius ICM-shell variable.
Examples:
display ball a_//ca # does not make much sense
See also:
xstick
an extended conformation ("E" in one-character notation).
Referred to as 'b' in
variable restraint
names: e.g. beta-zone for alanine is called "ab".
See also:
assign sstructure
,
set vrestraint
and file
icm.rst
.
See REBEL .
See also:
electroMethod,
delete boundary,
show energy",
term "el",
Potential( ).
is an acronym for the Biased Probability
Monte Carlo
method (
Abagyan and Totrov, 1994
). The method is based on a theorem establishing that
if the Monte Carlo procedure is used for global
optimization, rather than generation of a Boltzmann
ensemble, random moves based on known local probability
distributions (e.g. alpha and beta regions for
peptide backbone conformations) maximize the
optimization efficiency. Practically, the procedure
randomly choose a group of coupled angles
and changes them according to probabilities defined in
the
icm.rst file. Do not forget to
use the
set vrestraint a_/* command
before the
montecarlo command to activate
the biasing.