On Dec 8, 2004, at 10:13 AM, Elaine Meng wrote:
open your PDB file of interest run addh (note the aspartic acid is not protonated in this step) Tools... Utilities... Define Attribute (open the previously prepared input file) now run addh again (note the aspartic acid will be protonated)
Wanted to add one little addendum. In the current version of Chimera (1.2056), the first "addh" (before the Define Attribute) is actually necessary -- it is necessary to force Chimera to compute the atom types before overriding them with your own. This will be corrected in the upcoming production release in mid/late December. There are other ways to force the computation besides addh; finding h-bonds or going into ball-and-stick mode (the atom radius depends on the atom type) are a couple of other ways. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu