Ian Kerman ikerman at
Tue Jan 13 11:11:52 PST 2009

I used the pdbqt_to_pdb script in the utilities24 folder to convert one
of my ligands and when I opened it up in Chimera, the ring structure is
open. I opened the new pdb file in ADT and it shows a closed ring, as
does VMD, so I believe it's a difference in the rendering of the pdb
file. Has anyone else had this issue, and if so, how did you fix it? Is
there a way to export the connection info into the pdb file, which I
think may fix the issue? I've attached a picture illustrating the
problem. I've also submitted a bug request to Chimera since VMD seems to
be able to render it correctly. Thanks!



Ian Kerman

Research Associate


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