[phenixbb] phenix.pdbtools
Pavel Afonine
pafonine at lbl.gov
Thu Jul 18 10:19:35 PDT 2019
Hi Raja,
phenix.geometry_minimization model.pdb selection='chain A and resseq 1:123'
Pavel
On 7/18/19 09:37, Raja Dey wrote:
> 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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