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integrativemodeling / mediator

Modeling of the yeast Mediator complex
https://salilab.org/mediator/
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Sequence for med5 #2

Closed benmwebb closed 8 years ago

benmwebb commented 8 years ago

I'm a bit puzzled about the model for the med5 subunit. The FASTA file contains 1132 residues, but the Python script says

 ("med5", "med5_1", 0.40, fastadirectory+"med5.fasta", "med5", "BEADS", None, (1,1146,0), True, 40, 15, [19,12,15], 0, None, None, [15]),

i.e. a residue range of 1-1146. So as far as I can tell it adds extra beads to the end of the model (the S chain) to account for an extra phantom 14 residues. Am I reading that right?

mtrnka commented 8 years ago

Ahh... this seems to just be a typo/bug. With the beads size being 40 though, I don't think it actually added any extra beads, there should be 29 either way.

benmwebb commented 8 years ago

Ah yes, you're right, the C terminal bead just ends up being a little bigger than it should be - probably doesn't affect the modeling much.