Hi Qianyi, The command to replace an atom is "replace". It replaces the currently picked atom, the command for picking is "edit". Example:
edit first (resn ALA & name CB) replace H, 1, 1 See also: https://pymolwiki.org/index.php/Replace Cheers, Thomas > On May 2, 2017, at 5:49 PM, Qianyi Cheng <milochen...@gmail.com> wrote: > > I want to run QM calculation on reaction center of a large protein. So I need > to chop off many parts of the protein. I want to replace some side/main > chains with H atoms (for example replace the CB atom by a H atom and also > modify the C-H bond to the correct length). > I know how to make it work by clicking the build panel. But is there a way I > can write a script to make this happen? Thanks? -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
