I have a little XPLOR ascii-format electron density map reader worked
out. Can someone send me a few files?
I need a molecular coordinate file and the corresponding Xplor electron
density map.
I'm not sure exactly what the file format description is telling me:
Example format for Xplor Maps:
2 !NTITLE
REMARKS FILENAME=""
REMARKS scitbx.flex.double to Xplor map format
24 0 24 120 0 120 54 0 54
3.20420E+01 1.75362E+02 7.96630E+01 9.00000E+01 9.00000E+01 9.00000E+01
ZYX
0
-2.84546E-01-1.67775E-01-5.66095E-01-1.18305E+00-1.49559E+00-1.31942E+00
-1.01611E+00-1.00873E+00-1.18992E+00-1.02460E+00-2.72099E-01 5.94242E-01
<deleted>
-9999
0.0000E+00 1.0000E+00
That is:
...a blank line
...an integer giving the number of title lines, with mandatory !NTITLE
...title lines in %-264s format
...X, Y, and Z sections giving:
N sections per unit cell, in the given direction
Nmin ordinal of first section in file
Nmax ordinal of last section in file
[so, is a section a point, or are there N+1 points for N sections?]
[what if the first ordinal is not 0? What does that mean?]
[is it always true that Nmin + N = Nmax ?]
...unit cell dimensions
[do these have to be orthogonal? (I'm guessing not --- doesn't matter to
me, just wondering)]
...slow, medium, fast section order, always ZYX
[happy about that]
...for each slow section, the section number
...sectional data in special fortran format shown
[looks simple enough to me]
...-9999
...map average and standard deviation
Bob Hanson wrote:
>Jonathan Ouellet wrote:
>
>
>
>>Hi,
>>
>>
>>I would like to overlay a density map over a pdb model in Jmol so that
>>I could happily put it on the web.
>>
>>However, I saw that Jmol handle only gaussian cube density maps.
>>
>>Unfortunately, I don't have access to that expensive software (and I
>>don't really know what it is).
>>
>>I was wondering if there is a way to convert to .cub, or ideally,
>>insert a CCP4 or xplor density map in Jmol ?
>>
>>
>
>
>I'd love to get CCP4 or explor density maps in Jmol.
>
>Send me some sample files -- the PDB model, the density maps, any
>information you have about format -- and I will do it.
>
>Bob
>
>
>
>>cheers
>>
>>jo
>>
>>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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