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Dear Pavel and Sobolev,
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.
I overcome this problem by writing scrip which generate the selection suitable for phenix (chain and resseq).
Thank's Pavel for the link. Do you have somewhere the full list and description of available syntax keywords, not only examples?
Best regards,
Agnieszka
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 <[email protected]> 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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