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

Schulz, Eike-Christian eike.schulz at mpsd.mpg.de
Wed Mar 28 00:59:21 PDT 2018

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,


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


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.

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.


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,


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