source: branches/lib/HELP_SOURCE/source/rna3d_general.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.9 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      rna3d_manual.pdf
5
6#       sub topics:
7#SUB     subtopic.hlp
8SUB     rna3d_dispMolecule.hlp
9SUB     rna3d_dispBases.hlp
10SUB     rna3d_dispHelices.hlp
11SUB     rna3d_mapSeqData.hlp
12
13# format described in ../help.readme
14
15
16TITLE           RNA3D - molecole structure viewer
17
18                Visualization of Three-dimensional
19                structure of small subunit (16S) rRNA
20
21OCCURRENCE      In Primary Sequence Editor (ARB_EDIT4)
22
23DESCRIPTION
24
25    This program (RNA3D) displays the three-dimensional structure of small subunit (16S)
26    rRNA in OpenGL 3D environment. The annotation of RNA three-dimensional structures
27    consists of a preprocessing of the information embedded in their 3D coordinates. It
28    processes PDB structural information stored in the PDB file (1M5G) and used for
29    further structural analysis and searches. To provide user with the more detailed
30    perspective of 16S rRNA structure, structural information corresponding to the
31    ribosomal proteins were excluded during processing. The extracted structural information
32    is then fed to OpenGL engine, where it is further transformed into a hierarchy of
33    OpenGL objects, which encode molecule chains, residues and base positions. At this
34    stage, further processing may occur, for example when the user requests the mapping of
35    secondary structure information of rRNA onto the molecule in the form of loops and
36    stems. Any information derived from the multiple alignments (phylogenetic information)
37    is merged into the structural information or rRNA molecule in the post-processing
38    step.
39
40NOTES
41
42    More information regarding merging secondary structure information and mapping
43    individual rRNA sequence,sequence associated data, oligo-nucleotide probes can be found
44    in the respective help files. See "Subtopics" section.
45
46EXAMPLES        None
47
48WARNINGS        None
49
50BUGS            No bugs known
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