On Sep 15, 2011, at 10:11 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
I'm sure the Python script will work for you. However, it should be easy enough to select the B alternative positions with "@.b" and then use "Actions > Atom/Bonds > delete" to wipe them out. Then save the new PDB file. This will do exactly the same thing as the script you identified and may be easier for you.
If you want to consider occupancy values, you may have to manually inspect the PDB file yourself. But maybe Elaine can come up with a clever way to do that in Chimera...
You can use the Dock Prep tool (in Surface/Binding Analysis) to eliminate the lower-occupancy alt locs. Or for these 50/50 alt locs, to get down to just one of the two. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu