[Chimera-users] TER characters between residues in exported PDB ?

[Eric Pettersen]

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.

Hi Marek,
	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
		PDBio.addStandardResidue(r.type)

Then simply save your PDB file.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120607/bbca7941/attachment.html>