Oh, it's better than that!
I got the XPLOR files to work. An interesting aspect of these electron
density maps is that they can be HUGE and very tight grids on the order of
200x200x200 points. Two new aspects of Jmol make this NO PROBLEM:
1) Jmol now reads all grid-based data files "progressively" meaning only a
bit of information at a time. (Prior to this it loaded the whole grid into
memory -- now it's just a slice at a time, saving immense amounts of
memory.)
2) Jmol now allows loading of a subset of the data using the BOUNDBOX
parameter:
isosurface BOUNDBOX "xplor.map"
What this does is only create a map for the limits of the currently defined
boundbox -- which may be the standard "all atoms" one or may be one based on
whatever the user wants - for example, just around a helix, with a bit of
room to spare:
boundbox scale 1.1 {structno=2}
isosurface BOUNDBOX "xplor.map"
(same idea as the new draw BOUNDBOX or draw BOUNDBOX INTERSECTION)
I added this because in the case I was looking at there are 6 proteins in
the unit cell, and the XPLOR data included the entire unit cell. This way
you can truncate that to where you really have atoms.
This works extremely well.
I'll get this finished up shortly and out for checking.
Bob
On Thu, Jan 14, 2010 at 1:47 PM, Thomas Stout <[email protected]>wrote:
> Fantastic!! That will be an enormously impactful addition - I am
> quite excited to hear that -- the more non-crystallographers are
> exposed to actual experimental data, the better!! And, I think, the
> better they will understand concepts like resolution, mobility and
> disorder...
>
> -Tom
>
>
> Sent from a tiny virtual keyboard.
>
> On Jan 14, 2010, at 1:00 AM, Eric Martz <[email protected]>
> wrote:
>
> > Dear Tom,
> >
> > I cannot speak for the PDB, but I am currently in Israel
> > collaborating with the Proteopedia team, and that is why the renewed
> > interest in electron density maps -- so yes, Proteopedia will be very
> > interested when we succeed!
> >
> > -Eric
> >
> > At 1/13/10, Thomas Stout wrote:
> >
> >> Very exciting! This would be of enormous value (at least to me &
> >> the protein crystallography community). I should think the PDB &
> >> Proteopedia would be quite interested as well...
> >>
> >> -Tom
> >>
> >>
> >> On Wed, Jan 13, 2010 at 8:59 AM, Eric Martz
> >> <<mailto:[email protected]>[email protected]> wrote:
> >> I am again making an effort to render electron density maps (EDM) in
> >> Jmol, for protein crystallographic structures. If anyone else has
> >> done this, or has suggestions, please let me know!
> >>
> >> Jmol's script document list XPLOR as an input file format, but not
> >> CCP4 map format. So I assume the best way to proceed is to get the
> >> .hkl XPLOR EDM file and load it into Jmol. I haven't gotten that far
> >> yet, but I'm working on it.
> >>
> >> So far, it seems that the only EDM server I've found is at Uppsala
> >> (<http://eds.bmc.uu.se>http://eds.bmc.uu.se) and it generates O,
> >> CCP4, CNS, and EZD, none of which we think are .hkl XPLOR format. A
> >> crystallographer here says the XPLOR is an older, now less used
> >> format. Most people now use CCP4 .map format.
> >>
> >> The CCP4 version 6.1.0 program suite appears to have a bug in the
> >> conversion to XPLOR .hkl format, which omits the phases. I am
> >> currently downloading 6.1.3 to see if that bug is fixed.
> >>
> >> Thanks,
> >> --
> >> Eric Martz, Ph.D.
> >> Professor Emeritus, Microbiology, University of Massachusetts,
> >> Amherst
> >> <http://martz.molviz.org>http://martz.molviz.org
> >>
> >>
> >>
> >>
> >>
> >>
> >>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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