Copyright © 2020, Molsoft LLC
Nov 14 2024
| Contents |
|---|
| Introduction |
| Reference Guide |
| Command Line User's Guide |
| References |
| Glossary |
| A |
| B |
| base |
| ball |
| beta |
| blob |
| boundary element |
| BPMC |
| bfactor |
| C |
| D |
| E-H |
| I-N |
| O-R |
| S |
| T |
| U-Z |
| Index |
| Prev | ICM Language Reference B | Next |
[ base | ball | beta | blob | boundary element | BPMC | bfactor ]
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 .
blob |
Binary Large OBject (BLOB) can be used to store binary data. Blob can created by using read blob command or Blob function.
Example:
read blob "somebinary.icb" name="buf" Length(buf) String(buf,'base64') # to base64 String(buf,'hex') # to hex read binary input=buf # read ICB
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 chooses 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.
bfactor |
Crystallographic B-factor, also known as Debye–Waller factor or the temperature factor.
In models stored in PDB each atom has this parameter assigned along with x,y,z and occupancy.
Defined as 8π2 <u2> and measured in units of Å2 .
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