source: branches/lib/HELP_SOURCE/source/sec_display.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: 2.7 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           SECEDIT display options
12
13OCCURRENCE      ARB_SECEDIT/Properties/Display options
14
15DESCRIPTION     Here you can change various options:
16
17                  Display bases
18
19                    Toggle display of bases
20
21                  Distance between strands
22
23                    Sets the distance between opposite helix strands (default=1)
24
25                  Display bonds + Bond thickness
26
27                    Select whether/how to display bonds. You can choose to display
28                    bonds for non-helical parts in the middle of a helix region
29                    by selecting '+Non-helix'. Click the 'DEFINE' button to specify
30                    bond-types and their layout (see LINK{sec_bonddef.hlp}).
31                    'Bond thickness' defines the linewidth used to draw bonds.
32
33                  Annotate cursor
34
35                    Defines whether/how the current cursor position is annotated.
36                    If annotated, a small box containing a position number gets displayed.
37
38                    * None (=do not annotate cursor)
39                    * Absolute (=annotate with absolute alignment position)
40                    * Ecoli (=annotate with Ecoli-relative position)
41                    * Base (=annotate with base-number)
42
43                    The positions used are the same as displayed in
44                    the ARB_EDIT4 top-area (see LINK{e4.hlp}).
45
46                  Annotate helices
47
48                    If checked, each helix is annotated with its helix-number (as defined
49                    in SAI "HELIX_NR"; see LINK{helix.hlp}).
50
51                  Annotate ecoli positions
52
53                    If checked, every 100th ecoli position is annotated.
54
55                  Visualize search results
56
57                    If checked, hits from LINK{e4_search.hlp} get displayed in SECEDIT as well.
58
59                  Visualize SAI
60
61                    Toggle SAI visualization. See LINK{visualizeSAI.hlp}.
62
63                  Show all positions ...
64
65                    Any position where the sequence of the currently LINK{selected.hlp} has bases
66                    will always be displayed unconditionally.
67                    You can choose to additionally display
68                      * Binding helix positions
69                      * Ecoli base positions
70
71                  Display Structure Skeleton + Skeleton thickness
72
73                    Draw a skeleton of the secondary structure with variable line thickness.
74
75NOTES           Using the config-manager icon in the lower right corner of the window
76                will also handle the settings made in the 'Bond definitions' subwindow.
77
78EXAMPLES        None
79
80WARNINGS        None
81
82BUGS            No bugs known
Note: See TracBrowser for help on using the repository browser.