[phenixbb] atom selection syntax (fork Documentation in last Dev versions)

Alexander Batyuk batyuk at bioc.uzh.ch
Thu Mar 22 02:29:29 PDT 2012


Dear Ralf,

Now it's clear. Thank you!

Best wishes,

Alex



On 22 Mar 2012, at 10:08, Ralf Grosse-Kunstleve <rwgrosse-kunstleve at lbl.gov> wrote:

> These are boolean "and" and "or".
> "chain A and resid 1" selects all atoms with resid 1 in chain A, but not any atoms in chain B.
> "chain A or chain B" selects all atoms in chain A and (regular language) all atoms in chain B.
> Once you get use to it it makes total sense.
> Ralf
> 
> On Thu, Mar 22, 2012 at 1:04 AM, Alexander Batyuk <batyuk at bioc.uzh.ch> wrote:
> 
> Dear Nat,
> 
> Does that mean in your selection example that both chain A and chain C will be refined with anisotropic ADP or either one or another? I'm a bit confused with selection operator "or". And I was trying to put "and", which did not work.
> 
> Best wishes,
> 
> Alex
> 
> 
> On 21 Mar 2012, at 18:55, Nathaniel Echols wrote:
> 
> > On Wed, Mar 21, 2012 at 10:48 AM, Alexander Batyuk <batyuk at bioc.uzh.ch> wrote:
> >> Thank you, I'm trying to do a refinement in GUI and had to look up something in docs. Actually, I was looking for how to select say, chain A with residues 1-10 and all chain C for anisotropic ADP refinement in GUI? It seems that I can select only one chain with certain residues but not two.. Could you point me to the right direction, please?
> >
> > Hmm, not sure why this wouldn't work.  Are you using the graphical
> > editor or typing in the selection manually?  The editor seems to work
> > fine in "select range" mode (see image attached).  The selection
> > syntax is pretty simple too:
> >
> > (chain A and resseq 1:10) or (chain C)
> >
> > -Nat
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> 
> --
> Alex Batyuk
> The Plueckthun Lab
> www.bioc.uzh.ch/plueckthun
> 
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