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primaryodors / primarydock

PrimaryOdors.org molecular docker.
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Pepteditor: Helix function is warping side chains. #282

Open electronicsbyjulie opened 1 year ago

electronicsbyjulie commented 1 year ago

From this script:

GEN "ARNDCEQGHIKLMFPSTWYV"
HELIX ALPHA 1 20
SAVE "test/received/all20.pdb"

all20.pdb.txt

Can't seem to attach a PDB extension, but if rename the attachment from .pdb.txt to .pdb, can see in the viewer just how much it's distorting certain side chains, e.g. arginine, leucine, all four of the aromatics...

Doesn't happen if no HELIX command.

primaryodors commented 1 year ago

Since our predictions use ready-made PDBs, and therefore do not involve creating helices, this issue is not urgent.

electronicsbyjulie commented 1 year ago

It is happening even without helixing them.