Re: [PyMOL] label alternate conformations

[Seth H. <se...@gm...>]

Hi Bob,
Good to hear from you.

I didn't know about "alt" as a selection, so in the end that gave the
answer... Your example, which I find quite clever, didn't exactly match my
goal, though, so just to clarify:  Rather than distinguishing residues with
alternate conformations from those "normal" ones without, I wanted to have
the labels distinguish alternate conformer A from B and so on within a give=
n
residue. Since there was this backtick A or B at the end of the atom name i=
n
the right-click drop down menu I expected it would be somehow accessible vi=
a
command line in the label command. But "name" didn't do it. But of course,
using your "alt" selection I could do:
label alt a, "A"
label alt b, "B"
or indeed color all B conformations pink with:
color pink, alt b

And after realizing this, I just tried:

label myprotein, alt

which by its simplicity is obviously something I might have tried earlier.
Elegantly, as most residues don't have any "alt" conformation, it has the
nice side effect that labels only show up for those with alternate
conformations as well!

Thanks for the tip!
Seth

(By the way, neither the pymol help nor the wiki include "alt" as "symbols
defined in the name space" which currently includes things like "name, resn=
,
resi, b, q, segi, type, formal_charge, partial_charge, numeric_type,
text_type).  I guess that means I should learn to wiki it up.

On 12/7/05, Robert Immormino <imm...@gm...> wrote:
>
> This series of commands seems to do the job although a little sloppy.
>
> label alt a+"", "A%s-%s" % (resn, resi)
> label alt b+"", "B%s-%s" % (resn, resi)
> hide labels, alt ""
>
> Cheers,
>
> -bob
>
> On 12/7/05, Seth Harris <se...@gm...> wrote:
> >
> > Hi,
> >
> > I'm writing a small script to visit alternate conformations, stepping
> > through each as a frame in a movie with the cursor keys. I'd like to la=
bel
> > them to distinguish the alternates so I can see which I'd like to keep =
or
> > not, but:
> >
> > label alternates, name
> >
> > only displays the atom name without the pertinent `A or `B that the
> > right mouse click menu includes.
> >
> > Is there a way to show this information with the label command or other
> > means?
> >
> > Thanks,
> > Seth
> >
> > p.s. Those extra "3D" and other superfluous characters show up for me a=
s
> > well receiving the pymol list as a digest on gmail based web. I don't k=
now
> > if it's a result of the "digestion" process, but it seems like "=3D" si=
gns and
> > other non-alpha characters are associated with these burps of indigesti=
on,
> > invariably followed by 2D or 3D or such. I've kind of learned to ignore
> > them, but obviously they can cause some confusion and are at least mino=
rly
> > amusing when they reappear like some "who's on first" miscommunication =
as
> > warren's advice mention there should be no "3D" just the number "10" li=
ke
> > this, and then it proceeded to again display the 3D!! Perhaps the Diges=
t is
> > the culprit and could be treated? It also displays HTML as full text wi=
th
> > tags and all that garbage, by the way.
> >
> > >>>quote:
> > """I'm not sure where that "3D10" is coming from -- it should simply be
> > the
> > number 10:
> >
> > alter all, b=3D3D10
> > """
> > (!)
> > map_new can take a selection as its fourth argument, so you could
> >
>
>