Description

Comments and questions about defocus determination with ctffind3 and ctftilt.

Relion, CTFFIND and XDS

Hi,

I am currently trying to process several tiff micrograph images with relion. Once I get to the ctfffind step, I receive a puzzling message "cannot locate xds/nxds/xscale" although relion and xds/xscale can be started from the prompt (all software including relion, ctffind, and xds are located in /usr/local/bin)

What am I overlooking?

Kind regards,

Jeroen

Installing CTFFind-4.1.14

Attempting to install ctffind-4.1.14 on Centos8.3.   I have checked thoroughly that all dependencies are present.  I have tried all the compile versions which do not run (segmentation fault).   I compiled trying with --disable-debugmode the 'make' output has a lot of problems but runs to completion and I have attached the configure and make outputs:   (When I use --enable-debugmode there are far fewer warnings during 'make' but ctffind does not run  any further).   On running ctffind I get segmentation fault.

ctffind 4.1.14 compiling, wxWidgets curiosity and database.h lines

 

When compiling ctffind 4.1.14, I had two problems.

1. I had to rebuild wxWidgets without STL, otherwise my compiler (gcc) complained about trying to interpret wxStrings as const char *'s.

2. There seem to be a lot of lines in src/core/database.h which did not seem necessary, but caused grief like this:

Poor CTF fit due to ice

I am struggling to perform the CTF fitting due ice contamination. In a large proportion of my images, the CTF model fits the strong signal from the ice rather than the weaker Thon rings of the sample. I was wondering if there is a way to exclude the ice rings from the CTF correction (like in X-ray diffraction data)? I am using CTFFIND4 in Relion 3.1.

I have attached two examples of CTF fit, one where the fitting worked and one where it didn't.

Thank you for your help and best wishes,

Luca

build ctffind with OpenMP support

Hi all,

I built from source the latest cttfind (4.1.14) using openmp support on CentOS 7.5. To do so, I used the following configure command:

./configure --with-wx-config=`which wx-config` --enable-openmp

The build runs fine but when using ctffind, the resulting executable runs only on a single core. I did a ldd on the ctffind executable and I can see that it is linked against libgomp. When downloading and trying the precompiled binary, this one works fine with multi-core so yes it is possible to build ctffind with openmp support.

ctffind 4.1.14 segmentation fault

 

Dear All,

Recently I have installed ctffind-4.1.14 from ctffind-4.1.14.tar.gz, with exactly the following prerequisites satisfied"

sudo yum -y install epel-release

sudo yum -y install fftw fftw-devel wxGTK3 wxGTK3-devel libtiff libtiff-devel cmake make gcc git which diffutils gcc-c++ libjpeg-turbo-devel

My dataset was exactly the relion 3.1 tutorial dataset.Until and even at the ctffind step, the process was done exactly based on the relion 3.1 tutorial.

However the run.err of the ctffind step was as attached.

Segfault (4.4.14)

Firstly, thank you all for your work on ctffind.

The Error:

I'm trying to use ctffind with relion to determine the ctf of micrographs taken with a Leo912 scope. I'm experience segfault errors at multiple points.

1) If I run from inside Relion, I receive this output:

 

CtfFind4.1 loading mrc file error

I am a new user to relion and CtfFind and I've been encountering an issue with CtfFind on a set of mrc files. When I try to use CtfFind in Relion with these mrc files I receive the error:

WARNING: skipping, since cannot get CTF values for

Did not find any of the expected EPS files to generate a PDF file

+Will make an empty PDF-file in CtfFind/job002/logfile.pdf

When I look at the log file for CtfFind it says:

Error: File does not exist, please provide an existing file!

ctffind 4.1.14 segfault

 

Hi Alexis,

I'm running gcc version 9.3.0, Linux 5.6.11-arch1-1. So far I was unable to run standalone ctffind on any mic, the only working binary for me is from inside cistem (4.1.8 I believe)

1) the linux64 binary from the website segfaults straight away when I execute it.

2) I've downloaded the src, run ./configure --with-wx-config=/usr/bin/wx-config --enable-openmp --enable-debugmode then make. It produced the following output:

       **   Welcome to Ctffind   **