[phenixbb] phenix.pdbtools

Raja Dey rddey80 at gmail.com
Thu Jul 18 09:37:56 PDT 2019


Dear Members,
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
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