Re: [PyMOL] selecting Na+ in pymol

[Tsjerk W. <ts...@gm...>]

Hi Warren,

Actually, I tried to use select .., r. na\+ as the second option, but
that didn't work for me (Pymol 0.99b on Suse 9.2).

Oh, and I owe you an elaborate answer still on the mail from a while
ago. But that got a bit buried.. sorry ;)

Tsjerk

On 2/2/07, DeLano Scientific <de...@de...> wrote:
>
> Tsjerk & Abhinav,
>
> > Actually, it was a bit surprising to me to see you're right.
>
> + is the default list separator in selections.  For example:
>
> select posi, ARG+HIS+LYS/
> select backbone, n. N+CA+C+O
>
> That is why it needs to be escaped with a backslash.
>
> Commas can also be used, but only within parentheses -- otherwise the parser
> gets confused, since commas are also used to separate command arguments.
>
> select backbone, (n. N,CA,C,O)
>
> Also, be aware when using backslashes inside a Python string that they are
> also a string escape character, so it is best to use two of them "\\+".
> However, a single slash happens to work in this case for some bizzare
> reason.
>
> In other words, the PyMOL command:
>
> select selectionname, r. na\+
>
> has a true Python equivalent of
>
> cmd.select("selectionname","r. na\\+")
>
> not
>
> cmd.select("selectionname","r. na\+")
>
> which actually works, but probably shouldn't.
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf
> > Of Tsjerk Wassenaar
> > Sent: Friday, February 02, 2007 2:23 AM
> > To: Abhinav Verma
> > Cc: pym...@li...
> > Subject: Re: [PyMOL] selecting Na+ in pymol
> >
> > Hi Abhi,
> >
> > Actually, it was a bit surprising to me to see you're right.
> > Now, for showing/hiding, it has been dealt with in the code,
> > by allowing the "+" to be left out. However, for selecting
> > (and alter_ing) that doesn't go, apparently. A workaround is to use
> >
> > cmd.select("selectionname","r. na\+") or
> > cmd.select("selectionname","n. na\+")
> >
> > Alternatively, you can change the residue/atomnames using:
> >
> > cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'")
> >
> > All of these worked for me. Of course, it would be good to
> > have this dealt with properly in the same way as for showing/hiding.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On 2/2/07, Abhinav Verma <abh...@gm...> wrote:
> > > Hallo,
> > >  I have an annoying problem. I have pdb file with Na+ atoms
> > defined as
> > >
> > > ATOM      1 Na+  Na+    53      -1.106   7.854  52.244
> > 1.00  0.00         Na
> > >
> > > now if want to select these Na+ with
> > >
> > > PyMOL>select n. na+
> > >  Selector: selection "sele" defined with 0 atoms.
> > >
> > > Any ideas how to select them?
> > >
> > > I tried renaming them to Na and then select n. na which works. So I
> > > assume the problem is "+" which is used for add in pymol.
> > > I also tried n. "na+" which did not work either.
> > >
> > >
> > > thanks in advance,
> > > Abhi.
> > >
> > >
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
> > --------------------------------------------------------------
> > -----------
> > Using Tomcat but need to do more? Need to support web
> > services, security?
> > Get stuff done quickly with pre-integrated technology to make
> > your job easier.
> > Download IBM WebSphere Application Server v.1.0.1 based on
> > Apache Geronimo
> > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&
> dat=121642
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>
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623