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

[Agnieszka Kiliszek]

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

W dniu 10.02.2021 o 20:11, Oleg Sobolev pisze:
> Hi Agnieszka,
>
> _struct_asym.id <http://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 <http://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 
> <mailto: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
>     <http://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 <http://struct_asym.id>" in
>     phenix.polder?
>     >
>     > Best regards,
>     >
>     > Agnieszka
>     >
>     >
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*dr hab. Agnieszka Kiliszek*

*Zakład Struktury i Funkcji Biomolekuł*

Instytut Chemii Bioorganicznej Polskiej Akademii Nauk
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