ctffind3 fails on 32 Mb images

Submitted by Leo on Wed, 2015-02-04 12:59

Forums

ctffind & ctftilt

We collected some data from Krios which has updated EPU software
for Falcon II which outputs 32 Mb images instead of usual 64 Mb.
ctffind3 reports "Unknown format" for these images - is that a known issue?
Perhaps they will work with ctffind4? We had an issue of compiling ctffind4 for AMD so far.

Many thanks!
Leo

Alexis Wed, 2015-02-04 13:11

Hi Leo,

- the next version of ctffind4 (4.0.9; should be released in the next few days) should be compilable using GNU compilers (version >= 4.9.1). This should mean it'll be buildable under any platform using the free compilers from GNU.
- regarding the file format issue: probably if it doesn't work with ctffind3 it won't work with ctffind4. What format exactly are those images? If they are MRC/CCP4, please report the output of the header command (from IMOD or MRC package)

Hope this helps,
Alexis

Leo Wed, 2015-02-04 14:21

Hi,

Output of header.exe from MRC Image2010 is:

!!! Warning - architecture incompatibility !!!
!!! Fatal error - cannot read from or write to file : IN
!!! Use byte_swap_map followed by image_convert to reformat maps correctly !!!

But the images open OK in EMAN2.1 for particle picking and CTF correction and in Relion for picking.

Header info from e2iminfo:

FoilHole_23866371_Data_23853395_23853396_20150126_0455.mrc 1 images in MRC format 4096 x 4096
0.

HostEndian: little
ImageEndian: little
MRC.alpha: 0.0
MRC.beta: 0.0
MRC.gamma: 0.0
MRC.ispg: 0
MRC.machinestamp: 0
MRC.mapc: 0
MRC.mapr: 0
MRC.maps: 0
MRC.maximum: 0.0
MRC.mean: 0.0
MRC.minimum: 0.0
MRC.mx: 0
MRC.my: 0
MRC.mz: 0
MRC.nlabels: 0
MRC.nsymbt: 131072
MRC.nx: 4096
MRC.nxstart: 0
MRC.ny: 4096
MRC.nystart: 0
MRC.nz: 1
MRC.nzstart: 0
MRC.rms: 0.0
MRC.xlen: 1.0
MRC.ylen: 1.0
MRC.zlen: 1.0
apix_x: 1.0
apix_y: 1.0
apix_z: 1.0
changecount: 0
datatype: 4
is_complex: 0
is_complex_ri: 1
is_complex_x: 0
mean: 0.0
nx: 4096
ny: 4096
nz: 1
origin_x: 0.0
origin_y: 0.0
origin_z: 0.0
sigma: 0.0
source_n: 0
source_path: FoilHole_23866371_Data_23853395_23853396_20150126_0455.mrc
xform.projection: Transform({'tx':0.00,'ty':0.00,'alpha':0.000,'mirror':0,'scale':1.0000,'type':'2d'})

Thanks for any advice!
Leo

Alexis Wed, 2015-02-04 14:30

Thanks for the additional info. If you could share one such file with me (please email me), I will take a look & hopefully will be able to support this in the next ctffind4. If not, I will look for a workaround.

Thanks
Alexis

Alexis Thu, 2015-02-12 11:23

Ctffind 4.0.9, now available, should handle these files correctly and can be compiled using the GNU compiler (>=4.9.1).