[phenixbb] phenix.pdbtools

[Pavel Afonine]

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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