MultiSeq Help

File Menu -

• Choose work directory...: Displays a dialog for choosing the directory in which to place all MultiSeq-generated temporary files; these files are deleted on exit from MultiSeq
• 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 <original filename>.<index>.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

Help Menu -

• MultiSeq Help...: Opens the default web browser to this webpage

Selection -