ctffind & ctftilt

Hi Alexis,

I tried to call ctffind4 from the
command line on an mrc movie stacks with approx. 60 frames and faced the following
problem.

When I averaged over one frame, it just calculated the ctf for the first frame, when I
averaged over more frames it always gave me an output like this:

----------------------------------
Working on micrograph 1 of 1

100% [==============================] done!

**warning(Image::ComputeRotationalAverageOfPowerSpectrum): unable to
rescale 1D average of experimental power

Total execution time : 35 seconds

Hi,

I'm using CTFFind 4.0.15 and I had a problem posted previously on the forum where ctffind4 was not being able to write the Final values for some files. I decided to try to also give the "--only_do_unfinished" argument, which seems to be working great except that the .txt output file is not being written for these micrographs. Also, there is a (sometimes significant) difference between the log file value of the Thon rings fitting from the .txt output, is this information different or is one of them more accurate than the other? Thank you!

Hi, when running new ctffind4 4.0.16 version we noticed that for about 10-20% of images reported good fit of thon rings is only to 15-20 A, while previously for the same data it was to about 4-5 A (with ver 4.0.10). Looking at output it is clear that the fit itself is fine between 15 to 5 A with the new version, but background correction is thrown off at low resolution, so that quality of fit goes to 0 at about 20 A. We tried to change low resolution limits from 30 A (which was working fine for 4.0.10) to between 100 and 15 A, but it only gets worse.

Hello!

I've installed ctffind 4.0.16 on my OS X workstation (version 10.9.5) where I used gfortran (gcc5 5.1.0_1) to compile it.

The program works fine when I start it from terminal with no options, however when I use --old-school-input I get:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x103f05b26
#1 0x103f050c3
#2 0x7fff832065a9
#3 0x103f93dcf
#4 0x103d64b44
#5 0x103d651a3
#6 0x103daf0a2
#7 0x103db65de
Segmentation fault: 11

Hi all,

I am trying to use CTFFind 4.0.16 where I provide the input Fourier amplitudes (with background subtraction already performed). However there is some bug that renders the input into garbage and so the fitting fails.

The command line is as follows:

ctffind --amplitude_spectrum_input --filtered_amplitude_spectrum_input << STOP_PARSING
CTF4Input_cb580c2647bb8a66.mrc
CTF4Result_cb580c2647bb8a66.mrc
1.326
300.0
2.7
0.1
512
50.0
4.0
5000.0
35000.0
500.0
100.0
no
STOP_PARSING

Here is the input that I pass in as an MRC file (as float32):

Hi there!

I am tryiing to calculate the defocus on a set of images collected on a microscope with a Cs corrector, can CTFFIND4 handle a Cs=0.0?

I am getting the following error

ctffind4 --old-school-input
15may21z_May15_19.13.54_3145.mrc
15may21z_May15_19.13.54_3145-pow.mrc
0.0,300.0,0.07,59000.0,6.136,1
512,30.0,4.0,5000.0,35000.0,500.0,100.0
forrtl: error (73): floating divide by zero
Image PC Routine Line Source
ctffind4 00000000016B81B9 Unknown Unknown Unknown

Hello,

I'm trying to run ctffind4 and relion through the command line. Although I generated clean .log files for each .mrc file there is no output file all_micrographs_ctf.star. I'm including the errors below.

Thanks,
Matt

My command:
mpirun -n 4 `which relion_run_ctffind_mpi` --i "all_micrographs.star" --o "all_micrographs_ctf.star" --ctfWin -1 --CS 2 --HT 300 --AmpCnst 0.1 --XMAG 79096 --DStep 14 --Box 512 --ResMin 100 --ResMax 7 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 0 --ctffind3_exe "/home/mtherkel/ctffind --omp-num-threads 1 --old-school-input"
echo "done"

Dear Alexis/Niko

I haven't used either ctffind3 or ctffind4 before. I'd like to try the latter on a series of micrographs in a single step. Could you please tell me how to do so, or provide a script (I don't have much scripting experience)?

Thank you

Taha

To Whom It May Concern,

it seems that no matter what Fortran compiler I have in my PATH and specify on the configure line for FC and F77, e.g., Intel ifort (using 2013 distro) or gfortran (4.7.2), the configure program always fails when generating confdefs.h and exits with status 77 in its config.log. The output to the console says it cannot create executables, however if I try to touch files there as the uid running the build and it succeeds.

Hi,
I have been trying to install ctffind4.0.13 on both Mac OSx mavericks as well as linux ubuntu 12.10. Following the INSTALL configure command sudo ../configure FC=ifort F77=ifort I get the following error:
checking for Fortran 77 compiler default output file name...
configure: error: in `/usr/local/ctffind-4.0.13/build':
configure: error: Fortran 77 compiler cannot create executables
See `config.log' for more details.

log is attached

Is there some other way to configure?
Thank you,
Cheri