| Contents |
|---|
| Introduction |
| Reference Guide |
| User's guide |
| References |
| Glossary |
| A |
| B |
| C |
| D |
| E-H |
| S |
| T |
| U-Z |
| Index |
| Prev | 5.2 B | Next |
[ base | ball | beta | boundaryelement | BPMC ]
!- base 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.
!- ball 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 senseSee also: xstick
!- beta 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 .
!- boundary element
See REBEL . See also: electroMethod, delete boundary, show energy", term "el", Potential( ).
!- BPMC 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.
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