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AW: difference between FASTA and PDB



Hello YeBin,

Modeller states that you have more aminoacids in the alignment 
than in the pdb-file (353/352), and if you compare the fasta-sequence 
and the pdb-file you will find a lysine (K) at the C-terminus
that is not present in the pdb-file. Delete the K from your 
alignment or change it to a "-" and Modeller should work fine.

Remember that there might no be all aminoacids present in 
a pdb-file for structural reasons: loops at the surface may
be highly mobile, and can therefore often not be solved by 
crystallography, and that means you will have a gap in the 
structure. Before modelling, check the sequence. 

You can use DeepView to write out the aminoacids present in 
the pdb-file by loading the protein and then saving the sequence
in FASTA-format. 

Best wishes,
Thorsten