Hi Xiaobo,
As Elaine says, there is no command equivalent.  Of course, if you are willing to resort to Python you can do it.  I don’t know if you have any proficiency with Python or not, but if you do you would want to look at our Programmers Guide (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html) and in particular the “basic primer” for how to loop over files and do things in Chimera with those files (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html).
Then you would need to use the “changeAtom” function from the BuildStructure module to make your modifications.  You should work with a structure that has all its hydrogens present.  Given that, let’s say you want to modify hydrogen HG2 in residue 238.B.  To get its Python Atom instance:

from chimera import runCommand, selection
runCommand(“sel :238.b@hg2”)
a = selection.currentAtoms()[0]

then, to change it into a methyl group where the carbon is named ‘CM’:

from BuildStructure import changeAtom
from chimera import Element
changeAtom(a, Element(“C”), 4, 4, name=“CM”)

—Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Aug 26, 2015, at 1:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Xiaobo,
Sorry no, there is no command to add a chemical group in Chimera.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 26, 2015, at 10:53 AM, UCSF-xiaobowan <Xiaobo.Wan@ucsf.edu> wrote:

Hi all,
I am Xiaobo Wan, a postdoc at UCSF. I would like to learn how to add chemical groups (such as methyl) or change chemical atoms (Fluorine to Nitrogen) using the command in Chimera because I have thousands of compounds to do the same modification. I know the Build Structure in the Graphic interface can do this. I am not sure whether the addgrp command was supported by chimera now.
Best,
Xiaobo


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