ctffind & ctftilt

Hi,

I am running ctffind4 on CentOS7, and always get the following error message.
***************
**error(file_copy): io error 109 when writing to: .CTFFind.dff

Total execution time : 6 seconds

2016-07-13 09:50:07: Fatal error (file_copy): Write error
****************

But it works fine with root account.

Any idea?

thanks,

Huaibin

Hello,

I want use ctffind3 but I've a error message :

Warning: ieee_inexact is signaling
FORTRAN STOP

ctffind3.exe run normally when I use this alone.

Hi Alexis,

I have noticed that outputs from CTFFIND4 sometimes do not match each other. In particular, .txt file shows that ctf rings were fitted successfully only to 34A resolution, but the power spectrum for the same movie indicates much better results (Please see attached). The Nyquist is 5.24A. Would you trust the determined ctf parameters for such movies?

# Columns: #1 - micrograph number; #2 - defocus 1 [Angstroms]; #3 - defocus 2; #4 - azimuth of astigmatism; #5 - additional phase shift [radians]; #6 - cr

Alexis

Will Ctffind3 and 4 work with the rectangular frames from a DE camera> 5120 × 3840 pixels.

thanks.

C Akey
Prof.

Hi,
We recently collected some phase plate images with slight defocus and in the process of estimating the CTF.

What sort of amplitude contrast does one uses with these images and is it fine to use standard CTFFIND settings (meaning the default kV, ac but changing the range of focus) with the phase shift estimation set to yes.

Has the estimation of CTF from movie frames (as implemented in CTFFIND4 new version) been tried with phase plate images.

thanks

Vinoth

I had trouble running ctffind4.0.17 when it is called from the Relion 1.4 gui. When I run it with this in the Ctffind Executable box "/Applications/ctffind-4.0.17/bin/ctffind --old-school-input" in the , I got this output:

jjwwong$ Executing: mpirun -n 2 `which relion_run_ctffind_mpi` --i "all_micrographs.star" --o "all_micrographs_ctf.star" --ctfWin -1 --CS 2 --HT 300 --AmpCnst 0.1 --XMAG 39548 --DStep 14 --Box 512 --ResMin 100 --ResMax 7 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 0 --ctffind_exe "/Applications/ctffind-4.0.17/bin/ctffind --old-school-input" &

Optimal size of Fourier spectrum and aliasing

Hi Alexis,

in CTFFIND4 (Version - 4.0.17) what is the optimal size for the Fourier spectrum? I did 5 runs:

run01 fitting 30 - 4.5 unbinned 0.855 A/pixel 512 Thon rings with good fit up to : 4.9 Angstroms
run02 fitting 30 - 4.5 unbinned 0.855 A/pixel 1024 Thon rings with good fit up to : 5.4 Angstroms
run03 fitting 30 - 4.5 2 times binned 1.710 A/pixel 256 Thon rings with good fit up to : 5.0 Angstroms
run04 fitting 30 - 4.5 2 times binned 1.710 A/pixel 512 Thon rings with good fit up to : 5.4 Angstroms

Hello Alexis,

I am trying to run ctf estimation on relion1.4. I am using --omp-num-threads 1 --old-school-input in the executable.
However, when I run the ctf estimation I am not getting an output star file.
Do you by chance know how to go about fixing this?

Thanks

Hello all,

I have compiled ctfffind 4.0.17 using gfortran ( gcc 4.9.3 ) on a mac and it compiled OK with some warnings. I can use it in the interactive mode but I can't use it in the batch mode. I compiled with defaults suggested on the website along with LDFLAGS.

When I run it with ctffind --omp-num-threads 1 --old-school-input it still asks for

Input image file name [input.mrc] :

Anything obvious that I am missing during compiling ??

Thanks in advance for your help and time.

Rajan

Hi Alexis,

I'm new in this field. And I am trying to install the CTFFind4 on my Mac. I have a couple of questions in terms of installation.

Firstly, there are a couple of versions of CTFFind4? Which one is good for Mac with newest operation system.

Second, according to my understanding, the compilation will be different on Mac system than on a Linux system. And do you have a routine way to compile the version on Mac system?

By the way, I have successfully installed relion1.4 on my Mac.

Best,
Shijian.