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

[Georg Mlynek]

watch also the video tutorial under 
https://www.phenix-online.org/documentation/reference/atom_selections.html

around min 3.

Best, Georg.


Am 28.03.2018 um 12:02 schrieb Pearce, N.M. (Nick):
> 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 
> <eike.schulz at mpsd.mpg.de <mailto:eike.schulz at mpsd.mpg.de>> 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 
>> <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
>>
>> 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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>
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