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. | * 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] | * Submitted 1gi8 and the altered 3b8a to the Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] | ||
* 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 | * 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 identically 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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Turns out they are not the same protein; one is yeast hexokinase PI (3b8a) and the other is hexokinase PII (1ig8). | Turns out they are not the same protein; one is yeast hexokinase PI (3b8a) and the other is hexokinase PII (1ig8). | ||
According to help page for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment. Frustratingly, though it does seem to matter | According to help page for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment. Plus Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] says on the main page of the beta server, "this server will handle mutations and homologous sequences (only for proteins)." Frustratingly, though it does seem to matter. In the past, sometimes the files needed to be identical to me for anything to work on some versions of the Yale Morph servers. And unfortunately when it fails, it doesn't tell you why it failed or even that it failed. A lot of stuff they talk about never got implemented and maybe the alignment was part of it?<--NOPE, IT WAS A SERVER GLITCH. SEE NEXT TO SECTIONS. | ||
*THIS WHOLE AVENUE WAS UNNECESSARY BUT IT HELPED LEAD TO ISSUE.---To get so they were the same two proteins, I submitted the FASTA sequence of 3b8a (without amino acids 15-17) (that i got from PDBsum) to SwissModel and told it to homology model it to 1ig8. Got that result and called 3b8amodeledto1ig8.pdb | *THIS WHOLE AVENUE WAS UNNECESSARY BUT IT HELPED LEAD TO ISSUE.---To get so they were the same two proteins, I submitted the FASTA sequence of 3b8a (without amino acids 15-17) (that i got from PDBsum) to SwissModel and told it to homology model it to 1ig8. Got that result and called 3b8amodeledto1ig8.pdb | ||
