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Last change
on this file was
19532,
checked in by westram, 4 months ago
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- reintegrates 'help' into 'trunk'
- tweak arb documentation:
- automatically link
- ticket references to arb
 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
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Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.3 KB
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| 1 | # main topics: |
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| 2 | UP arb.hlp |
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| 3 | UP arb_ntree.hlp |
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| 4 | UP pfold.hlp |
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| 5 | UP glossary.hlp |
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| 6 | |
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| 7 | # sub topics: |
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| 8 | |
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| 9 | # format described in ../help.readme |
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| 10 | |
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| 11 | |
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| 12 | TITLE Create pfold SAI |
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| 13 | |
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| 14 | Import protein secondary structure and convert into SAI. |
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| 15 | |
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| 16 | OCCURRENCE ARB_NT/SAI/Create SAI using/Protein secondary structure |
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| 17 | |
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| 18 | DESCRIPTION |
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| 19 | |
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| 20 | Takes the currently LINK{selected.hlp} and searches for the field 'sec_struct'. |
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| 21 | A new SAI is created using the data in this field. A simple input window pops |
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| 22 | up where the default name '[species name]_pfold' for the new SAI can be |
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| 23 | changed. |
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| 24 | |
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| 25 | NOTES |
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| 26 | |
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| 27 | The import filter 'dssp_all.ift' allows for importing the amino acid |
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| 28 | sequence as well as the protein secondary structure from a dssp file and |
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| 29 | the structure is stored in the field 'sec_struct'. That way, secondary |
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| 30 | structure can be aligned along with the sequence manually and can later |
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| 31 | be extracted to create an SAI. |
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| 32 | |
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| 33 | The import filter 'dssp_2nd_struct.ift' extracts only the protein |
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| 34 | secondary structure which is stored as alignment data. SAIs can simply |
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| 35 | be created from these species using LINK{sp_sp_2_ext.hlp}. |
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| 36 | |
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| 37 | Refer to LINK{arb_import.hlp} and especially LINK{dssp_ift.hlp} |
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| 38 | for detailed information on importing sequences and structures and |
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| 39 | on the DSSP format. |
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| 40 | |
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| 41 | EXAMPLES None |
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| 42 | |
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| 43 | WARNINGS None |
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| 44 | |
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| 45 | BUGS No bugs known |
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