ctffind & ctftilt

we have a dataset of 860 .mrc files.

with the compiled binary from your site, some of the 860 processing jobs died.

therefore i recompiled your source with the intel 2013 suite (mkl, static).
DEST=${SW_HOME}/${PKG_NAME}/${PKG_VER}
FC=ifort F77=ifort \
./configure --prefix=${DEST} --enable-static
make -j ${BUILD_CPUS} 2>&1 | tee make.log

we can process at 2 sites:
export OMP_NUM_THREADS=1

1.) site 1 (scientific linux 6.5, AMD Opteron(tm) Processor 6380, there we made the executable)
from the 860 processes about 10 die (always the same datafiles) with

Hi,

I've been trying to get ctffind4 to work for my data. My initial tests seemed fine, especially using the default values, so it runs. Indeed it almost always runs, except when I use an amplitude contrast value of 0.05. Then I get the following error:

forrtl: error (65): floating invalid
Aborted

It works if I use 0.052 (so I have a workaround), but for some reason it doesn't like 0.05.

mike

Hello,

I tried using the script on my last ctf files generated with ctffind4 within relion, but I get the following error message and no file is written out.
We have on our cluster gnuplot and pdftk running. Am I doing something wrong or am I just missing something.

Cheers
Marcus

sh ../../ctffind/ctffind-4.0.7-linux64/ctffind_plot_results.sh align_14nov03a_XXX_XXX_00058gr_00055sq_v02_00019hl_00001en.frames_avrot.txt

Error: Unable to find file.
Error: Failed to open PDF file:
/tmp/tmp.pdf
Errors encountered. No output created.

To use ctffind4 from Relion 1.3, you need to supply ctffind with the "--old-school-input" command-line flag. You also need to surround the whole command with double quotes. Here is a simplified example from the command lien:

--ctffind3_exe "/lmb/home/tmartin/programs/ctffind-4.0.7-linux64/ctffind --omp-num-threads 1 --old-school-input"

Or from the Relion GUI, replace the executable by:
"/lmb/home/tmartin/programs/ctffind-4.0.7-linux64/ctffind --omp-num-threads 1 --old-school-input"

Hi,

The ctffind3_mp.exe binary produces the following error:

CTF DETERMINATION, V3.5 (9-Jun-2014)
Copyright 2013 Howard Hughes Medical Institute.
All rights reserved.
Use is subject to Janelia Farm Research Campus Software Copyright 1.1
license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html )

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

Backtrace for this error:
#0 0x456CCD in _gfortrani_backtrace
#1 0x4448C0 in _gfortrani_backtrace_handler
#2 0x48C8AF in __nptl_death_event
#3 0x0

Hi, we tried to install ctffind within appion but encountered an error that ctffind64.exe was not found at: /usr/lib/python2.6/site-packages
Would you advice on how to install it properly?
Thanks!
Chi-yu

I often like to compare CTF fits in a 1D plot (radial average). I can, of course, split the output image and compute the radial averages using other programs. Do you have any other suggestions for doing that or any plans to add 1D radial average output to CTFFIND3? Thanks.

I'm trying to use ctffind3 on OS X. I'm currently getting an error that I suspect is from reading the .mrc file. The .mrc file is output from EPU, which I suspect may have a format variation which is causing ctffind3 to not recognize it. I've tried using eman2/bsoft to convert the .mrc to another .mrc, and while ctffind3 appears to initially read the 'converted' file, it seems to hang soon afterwards. Do you have any suggestions on how I might go about getting ctffind3 to work?

My command file is:
./ctffind3_mp.exe << eof
original.mrc
power.mrc
2.7,300.0,0.07,129627.0,1.157

I am about to start processing my first data set collected as movies on a Falcon II using RELION and CTFFIND. When used together with RELION, the general approach seems to be to run CTFFIND on the average of all frames. However, I was wondering whether it is possible in CTFFIND to calculate a power spectrum from each frame separately, average these together and then estimate the CTF? I suspect in some cases, especially with very long exposures, this approach would give more accurate CTF estimates.

Hi Niko and lab!
Anchi and I are reviewing some ctf estimation results and noticed that when we specify a resmax of 10 angstroms, the image displaying simulated ctf from ctffind3 is limited to a resolution of about 15 angstroms.

Does this mean that it is really only fit using a 15 angstroms limit or could this be a display artifact?

Thanks, and California misses you!
Amber