OK, Eric, I found a couple of map files. Everything looks perfect to me, but
of course it needs testing. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip. Jmol
11.9.20_dev
WOW, I have to say, this is exciting. I want to learn more about electron
density maps! Jmol loads this one instantly:
isosurface color yellow within 2.0 {*} "c:/temp/3hyd_map.ccp4" mesh nofill;
reading isosurface data from c:/temp/3hyd_map.ccp4
FileManager opening c:\temp\3hyd_map.ccp4
data file type was determined to be MRC
FileManager opening c:\temp\3hyd_map.ccp4
MRC header: mode: 2
MRC header: dmin,dmax,dmean: -1.1890318,4.998787,-0.014114891
MRC header: ispg,nsymbt: 5,0
MRC header: rms: 0.74718976
MRC header: labels: 1
Created by MAPMAN V. 080625/7.8.5 at Fri Jan 15 04:34:50 2010 for A.
Nonymous
MRC header: bytes read: 1024
MRC/Jmol interpretation:
MRC/Jmol cutoff set to (dmean + 2*rms) = 1.4802647
grid parameters: nx,ny,nz: 38,90,55
grid parameters: nxStart,nyStart,nzStart: -11,-6,-11
grid parameters: mx,my,mz: 144,16,56
grid parameters: a,b,c,alpha,beta,gamma:
49.475,4.8375,19.4375,90.0,96.65,90.0
grid parameters: mapc,mapr,maps: 2,1,3
grid parameters: originX,Y,Z: 0.0,0.0,0.0
grid header: a,b,c,alpha,beta,gamma: 49.475,4.8375,19.4375,90.0,96.65,90.0
Jmol unit cell vectors:
a: (0.34357637, 0.0, 0.0)
b: (-1.3215866E-8, 0.30234376, 0.0)
c: (-0.040195342, -1.692914E-8, 0.34476298)
Jmol origin in unit cell coordinates: (-3.3371913, -1.8140624, -3.7923927)
Jmol use isosurface OFFSET {x y z} if you want to shift it.
Jmol origin in slow-to-fast system: (-1.8140624, -3.3371913, -3.7923927)
voxel grid origin:(-1.8140624, -3.3371913, -3.7923927)
voxel grid count/vector:55 -0.040195342 -1.692914E-8 0.34476298
voxel grid count/vector:90 0.34357637 0.0 0.0
voxel grid count/vector:38 -1.3215866E-8 0.30234376 0.0
JVXL read: 55 x 90 x 38 data points
VolumeFileReader reading data progressively
boundbox corners {-0.7172928 -0.3137546 -1.3790519} {25.194487 5.128433
12.066704}
VolumeFileReader closing file: data min/max/mean = -1.1890318, 4.998787,
-0.01760154
isosurface1 created with cutoff = 1.4802647 ; number of isosurfaces = 1
On Sun, Jan 17, 2010 at 12:26 PM, Robert Hanson <[email protected]> wrote:
> I'll need the xplor file. Not finding that...
>
> On Sun, Jan 17, 2010 at 11:50 AM, Eric Martz <[email protected]> wrote:
>
>> I found instructions here
>> http://www.ucl.ac.uk/~rmhasek/pymol.html<http://www.ucl.ac.uk/%7Ermhasek/pymol.html>
>>
>> for using a program called mapman to convert ccp4 electron density maps to
>> x-plor format. I think I did that, but my results in Jmol 11.9.19 were
>> unsatisfactory. You can see snapshots and download the map and other files
>> here:
>>
>> http://www.umass.edu/molvis/tests/jmol-edm-test2/
>>
>> Comments? Help?
>>
>> -Eric
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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.
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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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