Hi Bob,
I should have probably said that this is an EM map, not a crystallography one!
- Is JMol able to set absolute cutoffs (as normally required for EM
maps), rather than using relative sigma values?
- What is the default value of cutoff? The third object does display
1akeA_10A.mrc, so I’m not quite sure what you mean by saying that Jmol is
failing to read the file
Cheers,
Chris
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 05 September 2014 00:49
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Setting cutoff with some maps causes map to fail to
load
On Thu, Sep 4, 2014 at 1:28 PM,
<chris.w...@stfc.ac.uk<mailto:chris.w...@stfc.ac.uk>> wrote:
Following the examples on the jsmol.htm page, I tried to change the cutoff off
some maps I had; results at
www.ccpem.ac.uk/jsmol_test/cutofftest.htm<http://www.ccpem.ac.uk/jsmol_test/cutofftest.htm>
- The left hand object is the example, which works as expected
- The middle object has a direct replacement of the pdb and map files
from the example - note that the map file does not load (or, perhaps more
accurately, doesn’t display!)
The main problem is that Jmol cannot read
http://www.ccpem.ac.uk/jsmol_test/data/1akeA_10A.mrc
It reads the header fine (here without down-sampling)
reading nonstandard little-endian MRC file
MRC header: mode: 2
MRC header: nx ny nz: 22 22 22
MRC header: nxyzStart: 0 0 0
MRC header: na nb nc: 22 22 22
MRC header: mapc mapr maps: 1 2 3
MRC header: dmin,dmax,dmean: 0.0,0.4836611,0.037913516
MRC header: ispg,nsymbt: 0,0
MRC header: origin: {-6.494, 13.3810005, -5.41}
MRC header: rms: 0.0
MRC header: labels: 1
Chimera 1.3.2570 Mon Sep 7 14:15:16 2009
MRC header: bytes read: 1024
grid parameters: nx,ny,nz: 22,22,22
grid parameters: nxStart,nyStart,nzStart: 0,0,0
grid parameters: mx,my,mz: 22,22,22
grid parameters: a,b,c,alpha,beta,gamma: 66.0,66.0,66.0,90.0,90.0,90.0
grid parameters: mapc,mapr,maps: 1,2,3
grid parameters: originX,Y,Z: {-6.494, 13.3810005, -5.41}
Jmol unit cell vectors:
a: {3.0, 0.0, 0.0}
b: {-1.3113417E-7, 3.0, 0.0}
c: {-1.3113417E-7, -1.3113417E-7, 3.0}
Jmol grid origin in Cartesian coordinates: {-6.494, 13.3810005, -5.41}
Use isosurface OFFSET {x y z} if you want to shift it.
voxel grid origin:{-6.494, 13.3810005, -5.41}
voxel grid count/vector:22 -1.3113417E-7 -1.3113417E-7 3.0
voxel grid count/vector:22 -1.3113417E-7 3.0 0.0
voxel grid count/vector:22 3.0 0.0 0.0
JVXL read: 22 x 22 x 22 data points
reading data progressively -- yzCount = 484
boundbox corners null null
VolumeFileReader closing file: 10640 points read
data min/max/mean = -2.9817917E38/3.0790432E38/-Infinity
isosurface1 created with cutoff=0.5 min=-2.9817917E38 max=3.0790432E38;
isosurface count: 0
but then it reads garbage:
35224 -3.4932904E33
35228 -2.3340584E-14
35232 -2.289637E-14
35236 -5.3427773E9
35240 -4.4883956E7
35244 1.9568031E-32
35248 -3247113.8
35252 1.474E-41
What's the source of this file? Can you read it in by other MRC file readers?
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