[phenixbb] protein atom selection

Tristan Croll tic20 at cam.ac.uk
Fri Feb 3 11:59:04 PST 2017

Hi Wolfram,

I believe this is because Phenix (like most packages) uses a heuristic definition of "peptide" that's flexible enough to capture modified amino acids (even novel ones) - basically, anything that contains the canonical amino acid backbone (as SAM does) is captured. 



Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY


> On 3 Feb 2017, at 19:42, wtempel <wtempel at gmail.com> wrote:
> Hello all,
> in my hands and to my surprise, PHENIX atom selections such as "protein" or "peptide" would include a co-factor like SAM. Did others notice that also? Is this behavior what most users would want or even expect?
> Best regards.
> Wolfram Tempel
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