[Chimera-users] Re: [chimera-dev] add h

Eric Pettersen pett at cgl.ucsf.edu
Wed Dec 8 10:58:55 PST 2004

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 at cgl.ucsf.edu

More information about the Chimera-users mailing list