<div dir="ltr"><div class="markdown-here-wrapper" style=""><p style="margin:1.2em 0px!important">Hello Nigel,<br><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline">phenix.fetch_pdb 4yz8; phenix.pdbtools 4yz8.pdb keep="(protein)" modify.output.file_name=4yz8-protein.pdb stop_for_unknowns=False</code><br>Might the actual presence of a peptide bond (in the same chain, at least) be a reasonable requirement?<br>W.</p>
<div title="MDH:PGRpdj5IZWxsbyBOaWdlbCw8L2Rpdj5gcGhlbml4LmZldGNoX3BkYiA0eXo4OyBwaGVuaXgucGRi
dG9vbHMgNHl6OC5wZGIga2VlcD0iKHByb3RlaW4pIiBtb2RpZnkub3V0cHV0LmZpbGVfbmFtZT00
eXo4LXByb3RlaW4ucGRiIHN0b3BfZm9yX3Vua25vd25zPUZhbHNlYDxkaXY+TWlnaHQgdGhlIGFj
dHVhbCBwcmVzZW5jZSBvZiBhIHBlcHRpZGUgYm9uZCAoaW4gdGhlIHNhbWUgY2hhaW4sIGF0IGxl
YXN0KSBiZSBhIHJlYXNvbmFibGUgcmVxdWlyZW1lbnQ/PC9kaXY+PGRpdj5XLjwvZGl2PjxkaXY+
PGRpdj48YnI+PC9kaXY+PC9kaXY+" style="height:0;width:0;max-height:0;max-width:0;overflow:hidden;font-size:0em;padding:0;margin:0"></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Feb 3, 2017 at 3:01 PM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Wolfram<div><br></div><div>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. </div></div><div class="gmail_extra"><br clear="all"><div><div class="m_8729074950692846219gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : <a href="tel:(510)%20486-5709" value="+15104865709" target="_blank">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>Fax : <a href="tel:(510)%20486-5909" value="+15104865909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Feb 3, 2017 at 11:42 AM, wtempel <span dir="ltr"><<a href="mailto:wtempel@gmail.com" target="_blank">wtempel@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello all,<div>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?</div><div>Best regards.</div><div>Wolfram Tempel</div></div>
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