CYANA Command: angles ramachandran - Revision history

Guentert at 21:26, 12 August 2009

2009-08-12T21:26:28Z

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	For example:		For example:

	Ramachandran: # 1 5 10 15 20		Ramachandran: # 1 5 10 15 20
	SER 3 4 ..... . +.+ ....		SER 3 4 ..... . +.+ ....

	In this example, Ser 3 is in the disallowed region of the Ramachandran		In this example, Ser 3 is in the disallowed region of the Ramachandran

Guentert at 21:25, 12 August 2009

2009-08-12T21:25:41Z

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	== Parameters ==		== Parameters ==

	; selection=''~~string~~'': (default: ''none'')		; selection=''[[angle selection]]'': (default: ''none'')

	== Description ==		== Description ==

Guentert at 21:23, 12 August 2009

2009-08-12T21:23:46Z

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			''Ramachandran plot analysis''

	== Parameters ==		== Parameters ==

Guentert: /* Description */

2009-08-12T20:39:31Z

Description

← Older revision		Revision as of 22:39, 12 August 2009
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	allowed region of the Ramachandran plot.		allowed region of the Ramachandran plot.

	The '''angles ramachandran''' command can be complemented with the		The '''angles ramachandran''' command can be complemented with the '''ramaplot''' macro that produces a Ramachandran plot. The '''angles ramachandran''' command is included in the detailed overview produced by the '''overview''' macro.
	'''ramaplot''' macro that produces a Ramachandran plot. The '''angles
	ramachandran''' command is included in the detailed overview produced
	by the '''overview''' macro.

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

Guentert at 20:39, 12 August 2009

2009-08-12T20:39:05Z

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	== Parameters ==		== Parameters ==

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	The '''angles ramachandran''' command can be complemented with the		The '''angles ramachandran''' command can be complemented with the
	'''ramaplot''' macro that produces a Ramachandran plot. The '''angles		'''ramaplot''' macro that produces a Ramachandran plot. The '''angles
	ramachandran''' command is included in the detailed overview produced		ramachandran''' command is included in the detailed overview produced
	by the '''overview''' macro.		by the '''overview''' macro.

Admin: 1 revision

2009-01-29T11:26:54Z

1 revision

New page

== Parameters ==

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

== Description ==

Command that analyzes the PHI/PSI distribution of amino acid residues.
Only non-terminal amino acid residues with a selected PHI, PSI, OMEGA
and CHI1 torsion angle are analyzed, i.e. Pro and Gly are excluded. By
default, the selection made in the most recent '''angles select'''
command is used, or all angles if no selection has been made so far.

The PHI/PSI torsion angle value pairs are classified as lying in the
most favored, additionally allowed, generously allowed, or disallowed
regions of the Ramachandran plot, as defined by the program Procheck
(Laskowski et al., J. Biomol. NMR 8, 477-486, 1996). The percentage
of residues in each of these four classes is reported.

Amino acid residues for which the PHI/PSI pair of at least one selected
conformer lies in the generously allowed or disallowed regions of
the Ramachandran plot are reported in a table. The Ramachandran plot
regions are marked by ''blank'', '''.''', '''+''' and '''*''' for the most favored,
additionally allowed, generously allowed, and disallowed regions,
respectively.

For example:

Ramachandran: # 1 5 10 15 20
SER 3 4 *..... *. +.+ ....

In this example, Ser 3 is in the disallowed region of the Ramachandran
plot in conformers 1 and 9, in the generously allowed region in
conformers 12 and 14, in the additionally allowed region in 11
conformers, and in the most favoured region in the remaining 5
conformers. The '''#''' column reports the number of conformers in which
this residue is in an unfavourable, i.e., disallowed or generously
allowed region of the Ramachandran plot.

The '''angles ramachandran''' command can be complemented with the
'''ramaplot''' macro that produces a Ramachandran plot. The '''angles
ramachandran''' command is included in the detailed overview produced
by the '''overview''' macro.

== See also ==

* [[ramaplot]]
* [[overview]]