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 <[email protected]> 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:[email protected]
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf
> Of Tsjerk Wassenaar
> Sent: Friday, February 02, 2007 2:23 AM
> To: Abhinav Verma
> Cc: [email protected]
> 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 <[email protected]> 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
>
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> Get stuff done quickly with pre-integrated technology to make
> your job easier.
> Download IBM WebSphere Application Server v.1.0.1 based on
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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
