ctffind & ctftilt

I would like to ask you how ctffind3 generates a power spectrum (or is it an amplitude spectrum) from a large image by using a 512x512 block. Does the program average the power (amplitude) spectra generated as the 512x512 window is scanned over the large image?

Hi Axel,

Please see the attached image. I just realized that the cryo-scope we collected data on is a phase plate system. I don't know if this could have an effect.

Thank you!

-Chunfu

Dear Niko,

I have been trying to use ctffind3 to estimate the defocus of my cryoEM images. The parameters that i used are as follow:

CS[mm], HT[kV], AmpCnst, XMAG, DStep[um]
4.2, 200, 0.07, 106379.6, 15

Box, ResMin[A], ResMax[A], dFMin[A], dFMax[A], FStep[A], dAst[A]
256, 50, 4, 8000, 50000, 1000, 1000

and I get:
DFMID1 DFMID2 ANGAST CC

24050.82 21719.82 60.00 0.06457 Final Values

The right side of the output image showed hardly any thon rings(see attachment). I am wondering if the estimation is still reliable in this case.

I'm trying to figure out whether CTFFIND3 is able to estimate the CTF for a stack of images rather than for a single large image. After looking through the paper on CTFFIND3 and the Fortran code, my conclusion is that the program will not use a stack of images. Is this correct? Do you have a program that will use a stack of images to estimate CTF?

HI
I am using CTFFIND3.usually i don't get any error with the program but this time i ran it with fallowing options and it start to give me strange result.

i really appreciate it if some one help me to find out what i am missing and what are my mistakes.

------------------------------------------------------
:/fs/metawrk/pmohamma/nora_mrc_unbin> ctf3.com -m 62000 -s 7 -b 512 -d 3500 5000 500 -r 100 1 0 *u.mrc
Parameters for CTFFIND3
Spherical abberration : 2.0 mm

I have a user running CTFFIND3 release 20120506 on a 64-bit Red Hat 5.8 machine. Their command script looks like this:


/programs/x86_64-linux/ctf/20120506/bin/ctffind3.exe > ctffind3.log << EOF
image.mrc
new.ctf
2, 120, 0.1, 72000, 4480
512, 10, 100, 2000, 6000, 200
EOF


It spins for a few seconds and then seg faults. Running gdb on the core file gets me:

Reading symbols from /nfs/programs/x86_64-linux/ctf/20120506/bin/ctffind3.exe...done.
[New LWP 16855]

warning: Can't read pathname for load map: Input/output error.

Hi,

I get segmentation faults when running CTFTILT on tilted 2K and 1K CCD images. With a box size of 128 everything runs fine, but when I try box size 256 I get segmentation faults on most (but not all) of the images.

CTFTILT version is 1.5 from December 3 2010. I found a couple of threads regarding this error, but am not sure what to do, so before I start bugging our IT guy: Would a newer version make a difference or am I using weird parameters?

#!/bin/csh -x
ctftilt << eof
$1
$2
2.7,200,0.07,1,0.0003007,1
256,100.0,5.0,10000,50000,1000,$3,5
eof
#

Best,

Wim Hagen

Hi
I'm trying to estimate the defocs for a large set of image acquired on a titan Krios with CS correction and a falcon 4K DED camera (no scanner), original magnification is 75000, original pixel size is 0.88713 A.
the image are first coarse by a factor two resulting in a pixel size of 1.77426

I used the latest version of Ctffind3 with the following parameter
GridSquare_00079_FoilHole_0074_Data_0004_20120721_181019_c.mrc
GridSquare_00079_FoilHole_0074_Data_0004_20120721_181019_c_ctf.mrc
0,300,.07,75000,13.30695241497094
256,300,4,8000,50000,1000,100

So I have been searching for documentation about how to have CTFTILT logs its activity and/or implement error checking in some scripts based upon the exit code of the program. Can anyone help?

I have also seen CTFTILT rename the input file to ._filename and do some operation that effectively quartered the file size without printing any error/informational messages at all. What is it doing???

Hi,

on occasion I am getting very strange results for ANGAST, and it's causing me some grief tracking it down. It's not super frequent (2 micrographs of 98).

Here is the relevant output, as far as I can tell:

DFMID1 DFMID2 ANGAST TLTAXIS TANGLE CC
24619.03 25326.69 -1231.60 168.06 7.81 0.16212 Final Values

and it was generated with this input:

CS[mm], HT[kV], AmpCnst, XMAG, DStep[um], PAve
2.3 200.0 0.07 61404.0 7.000 2

Positive defocus values for underfocus