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