Jason,
but as I've understood super did alignment only for two structures, Is
there any way to do the same operation for ensemble ? (for CE as I
understood this could be done by alignto command but it lack for seq
alignment iin this case)
James
2011/11/21 Jason Vertrees <jason.vertr...@schrodinger.com>
> Hi James,
>
> > set fetch_host, pdbe
>
> Your PyMOL looks to be outdated. This was added to the open-source in
> v1.3r1, I think.
>
> > By the way could you also help me with the alignment of my structure (
> I've
> > posted this question today at this topic). I think that I should use the
> > combination of the structure alignment ( like CEalign) with the common
> seq.
> > alignment but I dont know exactly how :(
>
> You should use the 'cealign' or 'super' commands to do this. Cealign
> uses only structure, whereas 'super' uses both structure and sequence.
> Please continue to post questions like this to the list for best
> results: there are some very smart people on our PyMOL list.
>
> Cheers,
>
> -- Jason
>
> >
> > James
> >
> > 2011/11/21 Jason Vertrees <jason.vertr...@schrodinger.com>
> >>
> >> James,
> >>
> >> > 1) I've already tried to use it but the downloading was to slow. How I
> >> > can
> >> > change source for pdb downloading ? E.g set fetch_host didnt worked :(
> >>
> >> set fetch_host, pdbe
> >>
> >> should work. Please let me know if it doesn't.
> >>
> >>
> >> > 2) How I can specify individual chain for uploading via fetch command?
> >>
> >> You can't--PyMOL downloads the entire structure. To show just a given
> >> chain type something like:
> >>
> >> fetch 1hpv
> >>
> >> # "c. A" means "chain A"
> >>
> >> color blue, c. A
> >>
> >> Use similar selectors, for example
> >>
> >> # remove all atoms from the structure
> >> # except those in chain B
> >>
> >> remove not chain B
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrodinger, LLC
> >>
> >> (e) jason.vertr...@schrodinger.com
> >> (o) +1 (603) 374-7120
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
