[phenixbb] non-consecutive residue selection in phenix.polder
Pearce, N.M. (Nick)
n.m.pearce at uu.nl
Wed Mar 28 03:02:38 PDT 2018
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.
On 28 Mar 2018, at 09:59, Schulz, Eike-Christian <eike.schulz at mpsd.mpg.de<mailto:eike.schulz at mpsd.mpg.de>> wrote:
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!
From: "Pearce, N.M. (Nick)" <n.m.pearce at uu.nl<mailto:n.m.pearce at uu.nl>>
Date: Wednesday, 28. March 2018 at 09:49
To: "Schulz, Eike-Christian" <eike.schulz at mpsd.mpg.de<mailto:eike.schulz at mpsd.mpg.de>>
Cc: "phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>" <phenixbb at phenix-online.org<mailto: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”.
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:
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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