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