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
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
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 <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 <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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participants (3)
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Elaine Meng -
Eric Pettersen -
UCSF-xiaobowan