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<p>Dear Pavel and Sobolev,</p>
<p>Thank you for replay. Chain id select not only atoms of ligand
but also atoms of proteins assigned to this chain. The
_struct_asym.id is linked to _atom_site_asym_id. While the chain
name corresponds to _atom_site.auth_assym_id. Therefore it is not
possible to directly replace _struct_asym.id by chain name. <br>
</p>
<p>I overcome this problem by writing scrip which generate the
selection suitable for phenix (chain and resseq). </p>
<p>Thank's Pavel for the link. Do you have somewhere the <b>full</b><b>
list and description </b>of available syntax keywords, not only
examples?</p>
<p>Best regards,</p>
<p>Agnieszka<br>
</p>
<div class="moz-cite-prefix">W dniu 10.02.2021 o 20:11, Oleg Sobolev
pisze:<br>
</div>
<blockquote type="cite"
cite="mid:CADd3otFNqZm=KGK+Mp6EZUTKEoEuVr_dPKxPrLz9Q2Za0g+vKg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Agnieszka,<br>
<div><br>
</div>
<div>_<a href="http://struct_asym.id" moz-do-not-send="true">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"
moz-do-not-send="true">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"
moz-do-not-send="true">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"
moz-do-not-send="true">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" moz-do-not-send="true">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" moz-do-not-send="true">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" moz-do-not-send="true">struct_asym.id</a>"
in phenix.polder?<br>
><br>
> Best regards,<br>
><br>
> Agnieszka<br>
><br>
><br>
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