Eric and Tom,
Thanks for reminding me of the importance of this....
actually, CCP4 MAP file reading was included in 11.3.54, but I guess no one
caught on that "MRC" is the same as "CCP4". In any case, check out the
comparison at http://chemapps.stolaf.edu/jmol/docs/img/embd-1078.png.
There were some bugs there, so if you do want to use this, you will need to
get that file at
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
...unless you are talking about something different....
Bob
On Wed, Jan 13, 2010 at 12:09 PM, Thomas Stout <[email protected]>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 <[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) 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
>>
>>
>>
>>
>>
>>
>>
>>
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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
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