User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods: Difference between revisions

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 * First I changed chain X of 3b8a to chain A to match 1ig8 using [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies] for the protein. I knew PDB Goodies ignored and left out the heteroatoms so I changed the few lines of the glucose ligand to chain a by hand. The heterotoms will not be used by the Yale Morph server but I need them in the original file in order to be able to use fit or compare to add them in later.
 * Submitted 1gi8 and the altered 3b8a to the Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server]
-* When I received nothing back after several minutes I looked at the end of the sequences to see if they matched identially and noticed they didn't have the same C-terminus or even N-terminus. In fact what I thought were the same protein, according to FASTA sequence obtained for each PDB file from PDBsum, differ quite a bit:
+* TURNS OUT THIS NEXT ISSUE WAS NOT INVOLVED IN PROBLEM SO CAN SKIP TO TWO STEPS BELOW WHERE I WAS ABLE TO GET RESULT. ---When I received nothing back after several minutes I looked at the end of the sequences to see if they matched identially and noticed they didn't have the same C-terminus or even N-terminus. In fact what I thought were the same protein, according to FASTA sequence obtained for each PDB file from PDBsum, differ quite a bit:
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