That’s the difference between human logic and computer (Boolean) logic. “And” in the way you used it only selects atoms that are in BOTH residue 111 AND residue 222 (which is impossible as an atom can only be part of one residue). “Or” selects atoms that are in one OR the other. Thanks, Nick On 28 Mar 2018, at 09:59, Schulz, Eike-Christian mailto:[email protected]> 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)" mailto:[email protected]> Date: Wednesday, 28. March 2018 at 09:49 To: "Schulz, Eike-Christian" mailto:[email protected]> Cc: "[email protected]mailto:[email protected]" mailto:[email protected]> 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 mailto:[email protected]> 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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]

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)" *Date: *Wednesday, 28. March 2018 at 09:49 *To: *"Schulz, Eike-Christian" *Cc: *"[email protected]" *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 mailto:[email protected]> 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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