source: branches/lib/HELP_SOURCE/source/rna3d_dispHelices.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      rna3d_general.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Mapping Secondary Structural Information
13
14OCCURRENCE      In ARB primary structure editor (ARB_EDIT4) -> RNA3D
15
16DESCRIPTION
17
18    Secondary and tertiary structure interactions of the well established comparative
19    structure models of rRNA which are used in SECEDIT to generate 2D structure models are
20    fitted to the three-dimensional structure of E. coli master sequence.
21
22    DISPLAY HELICES:
23
24            Enabling this check box maps the secondary structural motifs (loops, helices
25            and bulges) onto the molecule. Secondary structural information is according
26            to the comparative models of rRNA used in primary and secondary structure
27            editors.
28
29    HELIX SKELETON:
30
31            Enabling will draw a skeleton of secondary structure mask.  By setting a grey
32            or light color you can achieve transparent mask avoiding any interference with
33            other information overlays.
34
35    DISPLAY MID-HELIX:
36
37            This displays middle point of the helices.
38
39    DISPLAY HELIX NUMBER:
40
41            Checking this box will display the corresponding helix numbers in the rRNA 3D
42            structure. Helix numbers are according to ARB numbering scheme.  The small
43            subunit (16S) rRNA of E.coli contains 50 helices which are numbered from 1 to
44            50.
45
46    DISPLAY NUMBER OF HELICES:
47
48            Using this you can set the number of helices you would like to be displayed in
49            the 3D molecule. This feature is very helpful to thoroughly examine the
50            specific helices in the structure.
51
52    HELIX SIZE:
53
54            Thickness or the size of the helices can be set by specifying the desired
55            value in this box.
56
57    DISPLAY TERTIARY INTERACTIONS:
58
59            The tertiary interactions observed in small subunit rRNA can be displayed in
60            the three-dimensional conformations of small subunit rRNA by enabling this
61            check box. The tertiary information data is from Gautheret et al.
62
63    Color settings related to helix, skeleton, mid-helix, helix number and tertiary
64    interactions can be changed using “Color Settings” of the main RNA3D window.
65
66NOTES
67               
68    Gautheret D, Damberger SH, Gutell RR: Identification of base-triples in RNA using
69    comparative sequence analysis. J Mol Biol 1995, 248: 27-43.
70
71
72EXAMPLES        None
73
74WARNINGS        None
75
76BUGS            No bugs known
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