I like to regularize the geometry of selected residues'
side chains using phenix.pdbtools? I couldn't find the
syntax. I used the following command line syntax, but didn't
work. Can someone help correcting this command?
phenix.pdbtools myprotein.pdb
geometry-regularization=true selection="((chain A and
((resseq 236:237 not backbone) or (resseq 240:241 not
backbone) or (resseq 244 not backbone) or (resseq 254 not
backbone) or (resseq 258 not backbone) or (resseq 261:262
not backbone) or (resseq 412:413 not backbone) or (resseq
416:417 not backbone) or (resseq 419 not backbone))) or
(chain X and ((resseq 104 not backbone) or (resseq 107:108
not backbone) or (resseq 111 not backbone) or (resseq 113
not backbone))))
Best regards,
Raja