Yes! All is good now.... Both the MRC and the O-format map files now load
and display correctly. Thanks very much for tracking this down, Bob -- it
was definitely a weird one.
-Tom
Here is the Java output:
FileManager.getAtomSetCollectionFromFile(3hyd.pdb)
FileManager opening /home/tstout/temp/jmol/jmol-12RC29/3hyd.pdb
The Resolver thinks Pdb
biomolecule 1: number of transforms: 4
Setting space group name to C 1 2 1
openFile(3hyd.pdb): 166 ms
reading 136 atoms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty
"auxiliaryInfo" to inspect them.
Default Van der Waal type for model set to Babel
Time to autoBond: 6 ms
ModelSet: autobonding; use autobond=false to not generate bonds
automatically
isosurface "3hyd_map.ccp4";
reading isosurface data from
/home/tstout/temp/jmol/jmol-12RC29/3hyd_map.ccp4
FileManager opening /home/tstout/temp/jmol/jmol-12RC29/3hyd_map.ccp4
0:38 1:0 2:0 3:0 4:90 5:0 6:0 7:0 8:55 9:0 10:0 11:0 12:2 13:0 14:0 15:0
16:245 17:255 18:255 19:255 20:250 21:255 22:255 23:255 24:245 25:255 26:255
27:255 28:144 29:0 30:0 31:0 32:16 33:0 34:0 35:0 36:56 37:0 38:0 39:0
40:102 41:230 42:69 43:66 44:205 45:204 46:154 47:64 48:0 49:128 50:155
51:65 52:0 53:0 54:180 55:66 56:205 57:76 58:193 59:66 60:0 61:0 62:180
63:66 64:2 65:0 66:0 67:0 68:1 69:0 70:0 71:0 72:3 73:0 74:0 75:0 76:50
77:50 78:152 79:191 80:16 81:246 82:159 83:64 84:37 85:66 86:103 87:188 88:5
89:0 90:0 91:0 92:0 93:0 94:0 95:0 96:0 97:0 98:0 99:0 100:0 101:0 102:0
103:0 104:0 105:0 106:0 107:0 108:0 109:0 110:0 111:0 112:0 113:0 114:0
115:0 116:0 117:0 118:0 119:0 120:0 121:0 122:0 123:0 124:0 125:0 126:0
127:0 128:0 129:0 130:0 131:0 132:0 133:0 134:0 135:0 136:0 137:0 138:0
139:0 140:0 141:0 142:0 143:0 144:0 145:0 146:0 147:0 148:0 149:0 150:0
151:0 152:0 153:0 154:0 155:0 156:0 157:0 158:0 159:0 160:0 161:0 162:0
163:0 164:0 165:0 166:0 167:0 168:0 169:0 170:0 171:0 172:0 173:0 174:0
175:0 176:0 177:0 178:0 179:0 180:0 181:0 182:0 183:0 184:0 185:0 186:0
187:0 188:0 189:0 190:0 191:0 192:0 193:0 194:0 195:0 196:0 197:0 198:0
199:0 200:0 201:0 202:0 203:0 204:0 205:0 206:0 207:0 208:77 209:65 210:80
211:32 212:68 213:65 214:0 215:0 216:212 217:71 218:63 219:63
data file type was determined to be MRC
FileManager opening /home/tstout/temp/jmol/jmol-12RC29/3hyd_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
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)
Jmol unit cell vectors:
a: (0.34357637, 0.0, 0.0)
b: (-1.3215866E-8, 0.30234376, 0.0)
c: (-0.040195342, -1.6929139E-8, 0.34476295)
Jmol grid origin in Cartesian coordinates: (-1.6193091, -3.325781,
-3.7923925)
Use isosurface OFFSET {x y z} if you want to shift it.
Cutoff set to (mean + rmsDeviation*1.0)
voxel grid origin:(-1.6193091, -3.325781, -3.7923925)
voxel grid count/vector:55 -0.040195342 -1.6929139E-8 0.34476295
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 {-3.6948903 -3.325782 -3.7923925} {28.958988 7.8609385
14.824806}
VolumeFileReader closing file: 188100 points read
data min/max/mean = -1.1890318, 4.998787, -0.01760154
isosurface1 created with cutoff=0.73307484 min=-1.1890318 max=4.998787;
number of isosurfaces = 1
PS --- Once every four years, the San Francisco Bay Area drifts back into
the US for election purposes. I'll have a check and see if I can set my
language settings accordingly! :)
On Fri, Jul 30, 2010 at 7:03 AM, Robert Hanson <[email protected]> wrote:
> OK, for the record.... this was a bug in the way Jmol was checking files to
> see what type they were. Thomas's local language settings were forcing Jmol
> to reading characters differently than mine, here in the US. I think I
> finally understand how to manage that. It should be corrected in what is
> uploaded now as http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol.jar
>
> Thomas, I need you to check that when you can.
>
> Bob
>
>
>
> On Tue, Jul 27, 2010 at 12:51 PM, Thomas Stout <[email protected]>wrote:
>
>>
>> I was having a look at electron density maps (MRC/CCP4 format) in Jmol
>> 12.0-RC26 (the application) and I get the following:
>>
>> $ isosurface color [x008000] cutoff 1.0 "3hyd_map.ccp4" mesh nofill;
>> isosurface1 created with cutoff=0.0 min=0.0 max=0.0; number of isosurfaces
>> = 0
>>
>> and nothing is displayed.If nature does not answer first what we
>> want,${workspace_loc:Jmol/bobtest}
>>
>
> --
> 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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