Re: [phenixbb] protein atom selection

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. ​ On Fri, Feb 3, 2017 at 3:01 PM, Nigel Moriarty wrote:

Wolfram

I 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.

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 <(510)%20486-5709> Email : [email protected] Fax : 510-486-5909 <(510)%20486-5909> Web : CCI.LBL.gov

On Fri, Feb 3, 2017 at 11:42 AM, wtempel 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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