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

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.lab...). 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 mailto:[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#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 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 > > > _______________________________________________ > phenixbb mailing list > [email protected] mailto:[email protected] > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: [email protected] mailto:[email protected]

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