Sequence Window : View Commands
Show titles
Causes the titles for each sequence to be displayed on the left side of the window.
These are on by default, but can be turned off by double-clicking the black separator
bar.
Show geometry violations
Shows in green background the places where a loop between aligned blocks is calculated
to be too short to span the distance between the the ends of these blocks, based
on the coordinates of the first structure of the alignment.
Find pattern
Finds and highlights all non-overlapping occurrences of a residue pattern. This
search uses ProSite syntax, described in detail at http://www.expasy.ch/prosite/
- see the description of the PA (pattern) syntax. For example, to search for lysine
separated by two to four residues from histidine, enter "k-x(2,4)-h";
unlike ProSite, the letters are case-insensitive, and a trailing period is not
required.
Cache highlights
Store the current set of highlights in a transient cache. The highlights will be remembered while the current file is being edited, but will not be saved in an output file and will not persist after Cn3D is exited.
Restore cached highlights
Restore the highlights from the transient cache, removing any existing highlights.
Show / hide rows
Show or hide specific rows of the alignment. All rows selected in the dialog will
be displayed. Note that because of the way Cn3D combines pairwise alignments,
especially when these alignments are very different (like from a VAST "multiple"
alignment of three or more proteins), when you hide rows the alignment of the
other rows may change. See the Cn3D Tutorial for more on this topic.
Show PSSM + contact scores
Calculate and display scores for each row based on alignment (PSSM) and contact
potential (structure-based) scores. You can specify what balance between PSSM
and contact potential to use. These values will then be displayed in the status
line at the bottom of the window when you move the mouse over each row.
Show self-hits
Calculates a BLAST alignment for each sequence in the current alignment, using
the PSSM constructed from the alignment, and restricting the alignment of each
sequence to its currently aligned range. Shows scores for each row, and
the percentage of rows that score significantly with the alignment's PSSM.
Export
Used to export the current alignment in one of several formats: FASTA
(with gaps), a2m FASTA, text, HTML (with color), or PSSM. The PSSM format is suitable for use with PSI-BLAST or RPS-BLAST.
Show taxonomy
Connects to the NCBI taxonomy server, and constructs the subset of the global
taxonomy tree that includes all sequences from the current alignment. In the
resulting taxonomy tree window, selecting a node and pressing space or return
will cause that node to be completely collapsed or expanded. Double-clicking
on a sequence node will highlight that sequence in the sequence window.
Highlight blocks
Highlight all the aligned blocks of the current alignment.
Expand highlights to aligned columns
If there are any highlights in an aligned column, then expand the highlights to all rows of that column.
Restrict highlights to row
Narrow down highlights to a selected row.
Clear highlights
Remove all highlighting.