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
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


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
Highlight Style Choose the display style for selection highlighting in the VMD OpenGL Display