<div dir="ltr">Hi Agnieszka,<br><div><br></div><div>_<a href="http://struct_asym.id">struct_asym.id</a> is linked with _atom_site.label_asym_id (<a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_asym_id.html">https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_asym_id.html</a>). In Phenix it becomes chain id, therefore the selection should look like "chain A" (use your _<a href="http://struct_asym.id">struct_asym.id</a> instead of "A").<br></div><div><br></div><div>Let us know if this doesn't work.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 10, 2021 at 9:17 AM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Agnieszka,<br>
<br>
currently the only way to make atom selections is to use Phenix atom <br>
selection syntax. To learn about atom selection syntax please refer to <br>
the following resources:<br>
<br>
<a href="http://phenix-online.org/documentation/reference/atom_selections.html#examples-for-selection-expressions" rel="noreferrer" target="_blank">http://phenix-online.org/documentation/reference/atom_selections.html#examples-for-selection-expressions</a><br>
<br>
Pavel<br>
<br>
<br>
On 2/10/21 05:18, Agnieszka Kiliszek wrote:<br>
> Hi everyone,<br>
><br>
> I would like to generate polder maps in phenix of selected ligand <br>
> molecules using mmCIF files. For me, the most convenient way of <br>
> selecting atoms of ligand was to use "_<a href="http://struct_asym.id" rel="noreferrer" target="_blank">struct_asym.id</a>". Therefore I <br>
> tried syntax selection segid but I received error "no atoms selected". <br>
> In pymol similar syntax "segi" works for the same mmCIF file.<br>
><br>
> What can be the reason of the error? Is it a way to select atoms of <br>
> ligand using "_<a href="http://struct_asym.id" rel="noreferrer" target="_blank">struct_asym.id</a>" in phenix.polder?<br>
><br>
> Best regards,<br>
><br>
> Agnieszka<br>
><br>
><br>
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