[Chimera-users] TER characters between residues in exported PDB ?
pett at cgl.ucsf.edu
Thu Jun 7 15:02:26 PDT 2012
On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
> Amber (Leap) automatically tries to create bonds between all
> consecutive residues unless they are separated
> by TER string.
So you're saying that if you take a completely standard PDB entry
from the RCSB that has water in it, and read that into Leap, Leap will
connect all the waters in a chain? Wouldn't it be better to ask on
the Amber list to have that behavior corrected so that all Amber users
could benefit from it?
Anyway, you can work around the issue in Chimera by forcing Chimera
to believe that all the residues in your structure are standard non-
HET residues. It will then write them out in ATOM records and place
TER cards between them when they're not connected.
Run this Python script (save to a file ending with .py and open it
with the "open" command or File->Open) with your structure open:
from chimera import Molecule, openModels, PDBio
for m in openModels.list(modelTypes=[Molecule]):
for r in m.residues:
r.isHet = False
Then simply save your PDB file.
UCSF Computer Graphics Lab
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