Multiple Alignment Quick Reference
File Menu
Choose work directory |
Displays a dialog for choosing the directory in which to place all
Multiple Alignment-generated temporary files; these files are deleted on
exit from Multiple Alignment |
Save work data to another directory |
Displays a dialog for choosing the directory in which to copy MultiSeq
files; these files are not deleted on exit
|
Write PDB from selection |
Writes pdb files corresponding to any selected residues; the highlighted
residues from each sequence go into a file named ..pdb (e.g. selections of a sequence from 1azu.pdb might
be called 1azu.0.pdb or 1azu.4.pdb) in the pdb directory; the index is
chosen so that all files written at the same time have the same index,
and no previous file is overwritten; user will be prompted to choose a
pdb directory in which to write the files |
Write alignment in FASTA format |
Writes a fasta file (multiseq.fasta) corresponding to the current
sequences whether they are aligned or not |
Write FASTA file with secondary structure data |
Writes a fasta file (multiseq.fasta) corresponding to the current
sequences whether they are aligned or not; STRIDE generated secondary
structure information is added below each sequence |
Tools Menu
Phylogenetic Tree |
Creates an RMSD- or Qh-based UPGMA tree
- Show Scale: Draws an appropriate scale beneath the tree
- Show Filename: Displays corresponding filename at exterior
nodes
- Show Species Name: Displays corresponding species at exterior
nodes; if the species name cannot be found, the filename is displayed
- Show Domain: Displays corresponding domain at exterior
nodes; if the domain cannot be found, nothing is displayed
- QH: Draws a phylogenetic tree based on Qh distances between
each pair of structures
- RMSD: Draws a phylogenetic tree based on RMSD distances
between each pair of structures
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Residue Selection |
- Q Value Selection is made based on Qalign score, Qa per
residue; choose the bounding score, S, (from 0 to 1) and whether you
want to select the residues with Qa >= S or Qa <= S
- Select: Make the selection; chosen
residues are highlighted in both the Sequence Display and the VMD OpenGL
Display
-
Close Window: Close the selection dialog
- Sequence Identity Selection is made based on sequence identity
score, SI; choose the bounding score, S, (from 0 to 1) and whether you
want to select the residues with SI >= S or SI <= S
-
Select: Make the selection; chosen residues are highlighted in both
the Sequence Display and the VMD OpenGL Display
- Close Window: Close the selection dialog
|
Number of Residues Per Molecule |
prints the number of residues per molecule |
Print QR Ordering |
prints the indices (starting with 0) of the current structures
corresponding to their relative linear independence, from most
independent to least independent |
RMSD Tools |
- RMSD Per Residue: Plots the RMSD per aligned alpha carbon
between each pair of selected proteins
- Pairwise RMSD: Prints the average RMSD for aligned alpha
carbons between each pair of proteins
|
Alignment Menu
Alignment Parameters |
- Number of passes (npass): Whether one or two fits are to be
performed. The idea is that the initial fit can be used with a
conformation biased set of parameters to improve the initial fit prior to
fitting using distance and conformation parameters. Default NPASS = 1
- Similarity (scanscore): Specifies how the Sc value (STAMP
algorithm) is to be calculated. This depends on the particular
application. As a general rule of thumb, use SCANSCORE=6 for large
database scans, when you are scanning with a small domain, and wishing to
find all examples of this domain - even within large structures. Use
SCANSCORE=1 when you wish to obtain a set of transformations for a set of
domains which you know are similar (and have defined fairly precisely as
domains rather than the larger structure that they may be a part of).
Default SCANSCORE = 6
- Number of comparison residues (scanslide): This is the number
of residues that a query sequence is 'slid' along a database sequence to
derive each initial superimposition. Initially, the N-terminus of the
query is aligned to the 1st residue of the databse, once this fit has
been performed and refined, and tested for good structural similarity,
the N-terminus is aligned with the 1+th position, and the process
repeated until the end of the database sequence has been reached. Default
SCANSLIDE = 5
- Slow scan: If set to TRUE, then the SLOW method of getting the
initial fits for scanning will be used (See chapter 1). Default SLOWSCAN
= FALSE
- Default Settings: resets the STAMP parameters to their
original values
|
Run Structural Alignment |
Calls STAMP to structurally align the proteins; superimposes
the aligned proteins and diplays them in the OpenGL Display window
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View Menu
Molecule Coloring |
- Q Per Residue: Colors the residues of each protein according
to their Qalign scores; proteins must be aligned first
- Sequence Identity Per Residue: Colors the residues of each
protein according to their sequence identity scores; proteins must be
aligned first
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Highlight Style |
Choose the display style for selection highlighting in the
VMD OpenGL Display |
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