[phenixbb] phenix.polder how to select atoms by _struct_asym.id

[Oleg Sobolev]

Hi Agnieszka,

_struct_asym.id is linked with _atom_site.label_asym_id (
https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_asym_id.html).
In Phenix it becomes chain id, therefore the selection should look like
"chain A" (use your _struct_asym.id instead of "A").

Let us know if this doesn't work.

Best regards,
Oleg Sobolev.

On Wed, Feb 10, 2021 at 9:17 AM Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Agnieszka,
>
> currently the only way to make atom selections is to use Phenix atom
> selection syntax. To learn about atom selection syntax please refer to
> the following resources:
>
>
> http://phenix-online.org/documentation/reference/atom_selections.html#examples-for-selection-expressions
>
> Pavel
>
>
> On 2/10/21 05:18, Agnieszka Kiliszek wrote:
> > Hi everyone,
> >
> > I would like to generate polder maps in phenix of selected ligand
> > molecules using mmCIF files. For me, the most convenient way of
> > selecting atoms of ligand was to use  "_struct_asym.id". Therefore I
> > tried syntax selection segid but I received error "no atoms selected".
> > In pymol similar syntax "segi" works for the same mmCIF file.
> >
> > What can be the reason of the error? Is it a way to select atoms of
> > ligand using "_struct_asym.id" in phenix.polder?
> >
> > Best regards,
> >
> > Agnieszka
> >
> >
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