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