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@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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