Hello Nigel,phenix.fetch_pdb 4yz8; phenix.pdbtools 4yz8.pdb keep="(protein)" modify.output.file_name=4yz8-protein.pdb stop_for_unknowns=False
Might the actual presence of a peptide bond (in the same chain, at least) be a reasonable requirement?
W.
WolframI can understand your surprise. I believe it's because the Monomer Library contradicts the Chemical Components and calls SAM an L-peptide. Can you describe how you are selecting so I can debug easily.CheersNigel---Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.govOn Fri, Feb 3, 2017 at 11:42 AM, wtempel <wtempel@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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