[phenixbb] non-consecutive residue selection in phenix.polder

[Pavel Afonine]

You can practice atom selection by using this command line utility

phenix.pdb_atom_selection model.pdb "(chain A and resseq 123:321) or 
(chain A and resid 345)"

that will show selected atoms on the screen.

Pavel

On 3/28/18 01:59, Schulz, Eike-Christian wrote:
>
> Dear Nick,
>
> Thank you very much for your quick reply. Indeed,  “or” worked very 
> nicely!
>
> phenix.polder model.pdb sf.mtz selection="resseq 111 or resseq  222"
>
> However, it escapes my understanding why
>
> phenix.polder model.pdb sf.mtz selection="resseq 111 and resseq  222"
>
> does not work equally well.
>
> Nevertheless, “or” does the trick!
>
> Many thanks,
>
> Eike
>
> *From: *"Pearce, N.M. (Nick)" <n.m.pearce at uu.nl>
> *Date: *Wednesday, 28. March 2018 at 09:49
> *To: *"Schulz, Eike-Christian" <eike.schulz at mpsd.mpg.de>
> *Cc: *"phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> *Subject: *Re: [phenixbb] non-consecutive residue selection in 
> phenix.polder
>
> Hi,
>
> Assuming it uses the standard phenix syntax you should be able to 
> string together a series of residue selections connected by “or”.
>
> See: 
> https://www.phenix-online.org/documentation/reference/atom_selections.html
>
> It should also be noted that any type of OMIT map will only show 
> “unambiguous” density for full occupancy ligands. If your ligands are 
> partial occupancy (which you generally can’t determine a priori), be 
> aware that you’ll be looking at a superposition of ligand density and 
> the other (unknown) state of the crystal.
>
> Thanks,
>
> Nick
>
>
> On 28 Mar 2018, at 09:42, Schulz, Eike-Christian 
> <eike.schulz at mpsd.mpg.de <mailto:eike.schulz at mpsd.mpg.de>> wrote:
>
>     Dear all,
>
>     To generate unambiguous ligand density in a number of structures
>     we would like to omit the surrounding active site residues in the
>     polder-map calculation. However, so far we were unable to figure
>     out how /non-consecutive/ residues can be selected for phenix.polder.
>
>     https://www.phenix-online.org/documentation/reference/atom_selections.html
>
>
>     The documentation only explains how to select ranges of residues
>     but not how to select say 5 individual residues.
>
>     Is there a syntax to achieve this ?
>
>     Thanks for your advice,
>
>     Eike
>
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