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.lab...).
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
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#exampl...
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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