Eric -- I found the test2 files (the link was still to test1.zip) and the
XPLOR. So what I find is that the CCP4 data is off by {0 0.6 0} relative to
the XPLOR data. Since these two readers use EXACTLY the same input
parameters, I have to assume that they really do not describe the exact same
density data. File CCP4 data is off by half a voxel. It would be interesting
to see how pymol does this.... OK, so I checked that out -- nothing special
there. Very odd....
Bob
On Sat, Jan 16, 2010 at 11:39 PM, Robert Hanson <[email protected]> wrote:
> Oh, good! That was just the example I needed. The other one I had did not
> have any remapping of axes, so that wasn't testable.
>
> Jmol 11.9.20_dev is at
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
>
> I think the match with Pymol is essentially perfect.
>
> Things to try, which are probably not possible with Pymol:
>
> # just around the molecule:
> load 3hyd.pdb
> isosurface color yellow within 1.6 {*} "3hyd_map.ccp4" mesh nofill
>
> # pretty much the full electron density data:
>
> load 3hyd.pdb {444 666 1} ; unitcell off; axes off
> isosurface color yellow "3hyd_map.ccp4" mesh nofill
> boundbox $isosurface1
> display within(boundbox)
> zoomto {displayed} 0
>
> Bob
>
>
>
> On Sat, Jan 16, 2010 at 2:55 AM, Eric Martz <[email protected]>wrote:
>
>>
>> I have done some tests attempting to load a small ccp4 format
>> electron density map in to Jmol 11.9.19_dev. The map loads and
>> surfaces are displayed, but "squashed" and not aligned with the
>> molecule. In contrast, the map looks correct and is aligned with the
>> molecule in PyMOL. I have put snapshots, the map.ccp4 file, the PDB
>> file, viewable online, and all downloadable in one .zip file, at
>>
>> http://www.umass.edu/molvis/tests/jmol-edm-test1/
>>
>> (Thanks to crystallographers Harry Greenblatt and Boris Brumshtein
>> for assistance.)
>>
>> -Eric
>>
>>
>>
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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,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
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,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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