Descriptor File Format
note: descriptor notes

The note record contains text distinct from the comments in a text descriptor file. Comments are removed when a descriptor is converted to binary and therefore are not recoverable when the binary file is converted back to text. The note record will survive the interconversion, although only one record will be visible.

The note record is echoed (typically to the monitor) whenever the descriptor is used. In particular, mimesis will echo the note record at the start of a simulation and exam will echo the note record when a descriptor file is opened. Thus the note record is a good place to document the molecular model contained in the descriptor file.

The note record has the format:

note
Nline
Lline

text...

...

The note record starts with the keyword note followed by the number of lines in the note Nline and the maximum width of the lines Lline. Immediately following this header line are Nline lines of text with the lines not exceeding Lline characters per line.

Example:


note 4 50   3DNA model of 10000 base pair random sequence plasmid. Created December 3, 1996 by DS, Biochem. Dept. UAB

In this example, there are four lines of text with each line not exceeding 50 characters. Note the first line is actually empty so only three lines of text appear. This could be a mistake but from now on these four lines (including the first blank line) will be echoed whenever the descriptor is used in mimesis or exam.


Details of Descriptor Records
intro
DES1
note
type
ivms
name
bond
mors
angl
angn
tors
itor
iton
nbn+
nbn-
ele+
ele-
vdw+
vdw-
abhb
noen
surf
stud
vlat
boun
lock

des format
arc format
yammp shell
exam commands
intro
arc
arcedit
arctransform
checkspider
des
elec2vlat

exam
mimesis
mkchainarc
mkchaindes
mkd3c
mkd3d
mkr2cc
mksnac
mksnad
xmd3
xmr2
ympf

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