https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Commands%3A_angles_ramachandranCYANA Commands: angles ramachandran - Revision history2026-04-20T04:01:41ZRevision history for this page on the wikiMediaWiki 1.45.1https://cyana.org/w/index.php?title=CYANA_Commands:_angles_ramachandran&diff=4460&oldid=prevAdmin: 1 revision2009-01-28T23:35:40Z<p>1 revision</p>
<p><b>New page</b></p><div><br />
== Parameters ==<br />
<br />
; selection=''string'': (default: ''none'')<br />
<br />
== Description ==<br />
<br />
Command that analyzes the PHI/PSI distribution of amino acid residues.<br />
Only non-terminal amino acid residues with a selected PHI, PSI, OMEGA<br />
and CHI1 torsion angle are analyzed, i.e. Pro and Gly are excluded. By<br />
default, the selection made in the most recent '''angles select'''<br />
command is used, or all angles if no selection has been made so far.<br />
<br />
The PHI/PSI torsion angle value pairs are classified as lying in the<br />
most favored, additionally allowed, generously allowed, or disallowed<br />
regions of the Ramachandran plot, as defined by the program Procheck<br />
(Laskowski et al., J. Biomol. NMR 8, 477-486, 1996). The percentage<br />
of residues in each of these four classes is reported.<br />
<br />
Amino acid residues for which the PHI/PSI pair of at least one selected<br />
conformer lies in the generously allowed or disallowed regions of<br />
the Ramachandran plot are reported in a table. The Ramachandran plot<br />
regions are marked by ''blank'', '''.''', '''+''' and '''*''' for the most favored,<br />
additionally allowed, generously allowed, and disallowed regions,<br />
respectively.<br />
<br />
For example:<br />
<br />
Ramachandran: # 1 5 10 15 20<br />
SER 3 4 *..... *. +.+ ....<br />
<br />
In this example, Ser 3 is in the disallowed region of the Ramachandran<br />
plot in conformers 1 and 9, in the generously allowed region in<br />
conformers 12 and 14, in the additionally allowed region in 11<br />
conformers, and in the most favoured region in the remaining 5<br />
conformers. The '''#''' column reports the number of conformers in which<br />
this residue is in an unfavourable, i.e., disallowed or generously<br />
allowed region of the Ramachandran plot.<br />
<br />
The '''angles ramachandran''' command can be complemented with the<br />
'''ramaplot''' macro that produces a Ramachandran plot. The '''angles<br />
ramachandran''' command is included in the detailed overview produced<br />
by the '''overview''' macro.<br />
<br />
== See also ==<br />
<br />
* [[ramaplot]]<br />
* [[overview]]</div>Admin