Array is not properly allocated

Submitted by yuhang on Sat, 2016-02-27 08:41

Forums

Unblur & Summovie

I have an unblur issue and wondering if there is any way to fix.

I collected some data directly with gatan DM program and saved as mrc stack. when I run the latest version 1.0.2 "unblur_openmp_7_17_15.exe" I got the following message
"2016-02-26 15:33:05: Fatal error (ImageFile::ReadSlicesFromDisk): Array is not properly allocated"

I also check the file by header and here is what I got:
################

[yhl@localhost ~]$header r_cc_0001.mrc

RO image file on unit 1 : r_cc_0001.mrc Size= 1333490 K

This is a byte-swapped file.

Number of columns, rows, sections ..... 3708 3836 24
Map mode .............................. 2 (32-bit real)
Start cols, rows, sects, grid x,y,z ... 0 0 0 3708 3836 24
Pixel spacing (Angstroms).............. 1.019 1.019 1.019
Cell angles ........................... 90.000 90.000 90.000
Fast, medium, slow axes ............... X Y Z
Origin on x,y,z ....................... 0.000 0.000 0.000
Minimum density ....................... -5.1346
Maximum density ....................... 91.210
Mean density .......................... 1.1425
tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0
Space group,# extra bytes,idtype,lens . 0 0 0 0

1 Titles :
Digital Micrograph(TM), GMS v 2.1f
###############
I am wondering is that because of the way that the file is saved? and do you have a way to fix it?

timgrant Mon, 2016-02-29 11:25

Hi Yuhang,

The file has been written byte swapped, which is a bit weird these days. At any rate, Unblur cannot handle byte swapped MRC files. You can use newstack from IMOD to convert it, just read it in and write it back out again and it should be readable by unblur, e.g. :-

newstack --input r_cc_0001.mrc --output r_cc_0001_swapped.mrc

Let me know if that doesn't solve your problem.

Cheers,

Tim