CCL: Monomer to Trimer

 Sent to CCL by: "Elaine  Meng" [meng-.-cgl.ucsf.edu]
 Hi Nahren,
 Many different programs can build a multimer from the monomer using matrix
 information in the PDB file.  The matrix information can be in SMTRY, CRYST,
 MTRIX, and BIOMT lines in the file.
 Ideally the authors would have put information on how to make the trimer in the
 BIOMT lines, but in this structure 2WKF that information is not included.
 Instead you can use the SMTRY information in the file to create the whole unit
 cell, which includes several trimers, and then get rid of all of the extra
 chains.  Another confusing thing about this structure is that it does have two
 copies of the structure, chains A and B.  When you create the unit cell, only
 the A chains of the different copies form the trimers.
 The program I work with is Chimera.  To do this in Chimera:
 - fetch 2wkf from the PDB (File... Fetch by ID)
 - Select chain B, remove it with Actions... Atoms/Bonds... delete
 - start Unit Cell (under Tools... Higher-Order Structure)
 - on that tool, click Make Copies, which will give 4 trimers
 Or you could make the copies first, and then delete chain B (multiple copies)
 but that would be messier.
 Chimera can be downloaded free of charge for any noncommercial use.
 http://www.cgl.ucsf.edu/chimera/index.html
 I hope this helps,
 Elaine
 -----
 Elaine C. Meng, Ph.D.
 UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
 Department of Pharmaceutical Chemistry
 University of California, San Francisco