#if CPP_PRG_STRAP
@*SBUT_HOWTO_DnD_RESSEL
You can use WIKI:Drag_and_drop to copy residue selections to other sequences or 3D-views
HTMLDOC_BUTTON:BUTS_MOVIE_Sequence_Features_in_3D!
*@
@*SBUT_MANY1ROW_DIA
For manipulating large numbers of homologous sequences simultaneously,
more than one sequence can be stacked in one single row.
Only one representative is shown while the other sequences are hidden.
When gaps are inserted or deleted manually or by alignment computations,
all sequences in that row are changed.
HTMLDOC_BUTTON:SBUT_MANY1ROW_DO!
HTMLDOC_BUTTON:SBUT_MANY1ROW_DO_CA!
For separating stacked sequences, select the row and press one of the two buttons.
*@
@*RSC_SBALLOON_ALIPANEL
The amino acid at the cursor position
- i: Residue index starting with 1
- c: Column (horizontal position) including gaps
- p Residue number in the structure (pdb) file
- n Nucleotide index and coding triplet
*@
@*RSC_SBALLOON_BUT_ALIGN
The selected or all sequences are aligned.
The alignment algorithm uses 3D-structures and sequences.
Hold shift to infer order.
If more control is required then use the Align-dialog instead.
Right-click button for context menu (Choose method, show details of last computation).
Current method:
*@
@*RSC_SBALLOON_ALIP_RESSEL
Handling:
- Drag-and-Drop: Residue selections can be dragged onto other sequences and 3D-structure views
- Right-click: The context menu provides many options.
- Double click: Edit annotations and associated 3D-rendering commands.
*@
@*RSC_HELP_DRAG_HETERO_COMPOUNDS
Use Drag-and-Drop to add hetero structures to protein
PDB-files containing only nucleotide chains or hetero compounds can be
dragged onto a protein label to associate the compound to the protein
Hetero compounds in list elements can also be dragged to another protein.
You may need to superimpose the source and target proteins to make coordinate systems compatible.
See Tutorial Copy
*@
@*RSC_HELP_DIA_COPY_RESSEL
Residue selections are underlined in the alignment panel.
Those that are selected have WIKI:marching_ants.
By pressing the button [Go], the residue selections are copied to the
target protein.
The variable V3DVAR_PROTEIN will be replaced by the name of the source sequence.
*@
@*RSC_HELP_DIA_NEWSEQ
The sequence name and the sequence data is entered.
The sequence of one letter codes can be entered directly or a one of several sequence file formats can be used.
HTMLDOC_SEE_CLASS:BUT_C1(ProteinParser).
*@
@*RSC_HELP_1ST_AMINO_IF_TRUNCATED
If the N-terminus of the sequence is chopped off,
the visible amino acid sequence is a subsequence of the total amino acid sequence.
If the check-box is activated,
the residue index for the first residue of the total sequence is set. See HTMLDOC_ITEM:M_P_CROP!.
*@
@*RSC_HELP_EXPLAIN_EXPORT_BY_DND
Sequences can be exported by dragging the sequence label to a file browser,
the desktop or onto other applications.
HTMLDOC_BUTTON:BUTS_MOVIE_Export_Proteins! WIKI:Drag_and_drop
Options can be changed: HTMLDOC_BUTTON:SBUT_DRAG_OPTS
Export using the context menu
Alternatively, the export-dialog can be used.
HTMLDOC_ITEM:BUT_C1(DialogExportProteins)
*@
@*RSC_HELP_EXPLAIN_SELECT_RESSEL
Selected residue selections are indicated by marching ants in the alignment pane.
Selecting residue selections in the alignment pane:
- Ctrl+left-click highlightings.
- Open a red-white rubber band around the underlinings.
*@
@*RSC_HELP_DIAALIGN_EXPLAIN_PROFILE
Enter a sequence alignment without sequence name which will be used as a profile.
More than one profile can be given. They need to be separated by a blank line.
A rectangular region ("walking ants") in the alignment pane can be inserted as a profile:
Specify a rectangular alignment region with the mouse. Right-click the red-white rectangle and select "Copy" in the context menu. Type Ctrl+V to insert.
*@
@*RSC_HELP_DIAALIGN_EXPLAIN_SEQLIST
The tabulator key completes sequence names.
Residue ranges are written in the form "myProtein/100-200".
If the range goes from the first or to the last position, it can be written like "myProtein/-200" or "myProtein/100-", respectively.
With the tool button below, residue ranges of residue selections can be copied.
The following dialogs can generate residue selections by computation:
*@
#endif //CPP_PRG_STRAP
@*~RSC_DIALOG_SEQ_ICON
Drag-and-Drop:
Image icons can be associated with sequences or annotations using Drag-and-Drop. Click
Drop_Web_Link* for more information.
Species Icons:
Organism names can be used to automatically select a suitable icon.
The following button acts on the selected sequences:
HTMLDOC_BUTTON:SBUT_SPECIES_ICONS!.
Structure Icons:
For selected sequences with a PDB-ID, the PDB thumb-nail images can be associated:
HTMLDOC_BUTTON:SBUT_PDB_ICONS!.
Remove: The following button removes the icons from all selected sequences:
HTMLDOC_BUTTON:SBUT_DEL_ICONS!.
Customize mapping of species and icons: HTMLDOC_BUTTON:CUSTOM_speciesIcons!
*@
@*~RSC_HELP_STRAP_ABOUT
Author: Christoph Gille
Home-page: HTMLDOC_URL:iURL_STRAP_SLASH
License: GPL
Compiled: CPP_UNSTRINGIZE(CPP_DATE) CPP_UNSTRINGIZE(CPP_HOUR_MINUTE)
In publications please cite PUBMED:24813445 and/or PUBMED:16322575
Used software:
- Icons 8 http://icons8.com/
- Some libraries from http://www.apache.org/ under Apache License.
You are running Java HTMLDOC_TEXT:SYS_JAVA_VM_NAME HTMLDOC_TEXT:SYS_JAVA_VERSION
*@
@*~RSC_STEXT_M_P_MENU_IMPORT
Import sequences by WIKI:Drag_and_drop as follows:
Drag a sequence file or sequence web link into Strap. See movie HTMLDOC_BUTTON:BUTS_MOVIE_Load_Proteins!
Not all web browsers support Drag_and_drop (Internet-Explorer) and you may need to try a different one.
*@
@*~RSC_HELP_STRAP_DRAG_DROP
Actions which are performed when objects are dropped on certain targets.
| D r o p p e d O b j e c t s (Also see WIKI:Drag_and_drop and Drop_Web_Link*) |
Drop target |
Sequences |
Residue selections |
Hetero groups |
Image files (png, gif, jpg) |
|
|
Copy residue selection to target sequence |
Add heteros to target protein |
Set icon image |
Drop on residue selections |
|
|
|
Set background image |
Drop in 3D-View |
Add 3D-structure to view |
Highlight atoms/amino acids in 3D |
Add hetero structure to view |
|
Drop in alignment panel |
Load sequence |
Add residue selection to sequence |
|
|
Drop in desktop or file browser |
Copy sequence file |
|
Export as single PDB-file |
|
See Drop_Web_Link*
*@