CYANA Command: grid correlate - Revision history

Masayo: /* Parameters */

2009-08-12T13:24:40Z

Parameters

← Older revision		Revision as of 15:24, 12 August 2009
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	== Parameters ==		== Parameters ==

	; function=''string'' (required)		; function=''string'': (required)
	; selection=''string'': (default: ''none'')		; selection=''string'': (default: ''none'')

Masayo: /* Description */

2009-08-07T11:39:24Z

Description

← Older revision		Revision as of 13:39, 7 August 2009
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	== Description ==		== Description ==

			Defines relationships between dihedral angles in a grid search. For instance, the dihedral angles of a sugar ring can be represented by a single degree of freedom, the pseudorotation angle.
			To represent a group of torsion angles as a single degree of freedom in a grid search, this command has to be called once for each correlated dihedral angle. If the ''selection'' matches exactly one angle within the fragment, then this dihedral angle will be related by the given ''function'', a Fortran expression of type real, to a variable, '''p'''. The variable '''p''' will be the single degree of freedom for the grid search during which it will vary from 0 to 2π. If exactly two angles within the fragment are selected, one of which has occurred in a previous '''grid correlate''' command, then the “new” angle will be correlated by the given ''function'' to the same parameter '''p''' as the "old" angle.

	~~This command defines relationships between dihedral angles in a grid~~
	~~search. For instance, the dihedral angles of a sugar ring can be~~
	~~represented by a single degree of freedom, the pseudorotation angle.~~

	~~To represent~~ a ~~group~~ of ~~dihedral angles as a single degree~~ of		For example, a molecular fragment consisting of the sugar ring of nucleotide residue 4 in a DNA or RNA molecule can be defined, and the dihedral angles of the sugar ring, DELTA, NU1, and NU2 be correlated to the pseudorotation angle, as follows:
	~~freedom~~ in a ~~grid search~~, ~~this command has to be called once for each~~
	~~correlated dihedral angle. If exactly one angle within the fragment~~
	~~is matched by~~ the ~~'''selection''' parameter, then this~~ dihedral ~~angle~~
	~~will be related by~~ the ~~given '''function'''~~, ~~a Fortran expression of type~~
	~~real~~, ~~to a variable~~, ~~p. The variable p will~~ be ~~the single degree of~~
	~~freedom during the grid search during which it will vary from 0~~ to
	~~2*pi. If exactly two angles within~~ the ~~fragment are selected, one of~~
	~~which has occurred in a previous~~ angle ~~correlate command~~, ~~then the~~
	~~"new" angle will be correlated by the given '''function''' to the same~~
	~~parameter p~~ as ~~the "old" angle.~~

	~~For example, a molecular fragment consisting of the sugar ring of~~		grid fragment DELTA NU1 NU2 4<br>
	~~nucleotide residue 4 in a DNA or RNA molecule can be defined, and the~~		numax=40.0/rad # amplitude; rad = 180/π<br>
	~~dihedral angles of the sugar ring, DELTA, NU1, and NU2 be correlated~~		grid correlate numaxcos(p+2pi/5)+2*pi/3 DELTA<br>
	~~to the pseudorotation angle, as follows:~~		grid correlate numaxcos(p-2pi/5) "DELTA NU1"<br>
			grid correlate numax*cos(p) "DELTA NU2"<br>
	grid fragment "DELTA NU1 NU2 4"
	numax=40.0*pi/180.0
	grid correlate numaxcos(p+4pi/5)+2*pi/3 "DELTA 4"
	grid correlate numaxcos(p-4pi/5) "DELTA NU1 4"
	grid correlate numax*cos(p) "DELTA NU2 4"

	== See also ==		== See also ==

	* [[sugarring]]		* [[sugarring]]

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

New page

== Parameters ==

; function=''string'' (required)
; selection=''string'': (default: ''none'')

== Description ==

This command defines relationships between dihedral angles in a grid
search. For instance, the dihedral angles of a sugar ring can be
represented by a single degree of freedom, the pseudorotation angle.

To represent a group of dihedral angles as a single degree of
freedom in a grid search, this command has to be called once for each
correlated dihedral angle. If exactly one angle within the fragment
is matched by the '''selection''' parameter, then this dihedral angle
will be related by the given '''function''', a Fortran expression of type
real, to a variable, p. The variable p will be the single degree of
freedom during the grid search during which it will vary from 0 to
2*pi. If exactly two angles within the fragment are selected, one of
which has occurred in a previous angle correlate command, then the
"new" angle will be correlated by the given '''function''' to the same
parameter p as the "old" angle.

For example, a molecular fragment consisting of the sugar ring of
nucleotide residue 4 in a DNA or RNA molecule can be defined, and the
dihedral angles of the sugar ring, DELTA, NU1, and NU2 be correlated
to the pseudorotation angle, as follows:

grid fragment "DELTA NU1 NU2 4"
numax=40.0*pi/180.0
grid correlate numax*cos(p+4*pi/5)+2*pi/3 "DELTA 4"
grid correlate numax*cos(p-4*pi/5) "DELTA NU1 4"
grid correlate numax*cos(p) "DELTA NU2 4"

== See also ==

* [[sugarring]]