VMD tutorial Part 02

Multiple Molecules and Multiple Alignment

 

Under construction

 

• http://www.scs.uiuc.edu/~schulten/tutorials/evolution/index.html Multiseq tutorial

1. run VMD
2. select VMD Main → Extensions → Analysis → MultiSeq
3. you wil be prompted to select a directory for storing Metadata. This will be used to store a number of NCBI databases that are required for the analysis of sequence/phylogeny/structure relationships. They include

• The CBI Taxonomy database
• A mapping between NCBI GIs and taxonomy (which organism does a GI come from)
• The enzyme nmenclature database
• A mapping of SWISS-PROT IDs to PDB
• SWISS-PROT to NCBI Taxonomy mapping

1. If the databases do not already exist on your machine, or need to be updated, MultiSeq will prompt you to download them. Click OK after the download is finished and close the preferences window.