Description

Comments and questions about defocus determination with ctffind3 and ctftilt.

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   **

ctffind 4.1.13

 

I have installed ctffind 4.1.13 from ctffind-4.1.13.tar.gz based on inside “REDME” and the message from “Error compiling version 4.1.13 on Linux –using pdb.h & water.h files” in the Forum. However, when I run relion 3.1 for the CTF estimation it gave run.err as attached (which I have converted to the doc format with the content exactly copied and pasted from run.err).

Relion did not find any of the expected EPS files

Hi,

I've been trying to use CTFFIND-4.1 to do CTF estimation in relion-3.0, but I have been unsuccessful due to relion not finding the expected EPS files. Each time, none are produced and the .star file made is empty.

I'm fairly certain I have compiled and installed CTFFIND 4 correctly on my OS but seem to be missing something. I have used CTFFIND3 before in relion-2.0 on another machine. I'm wondering if there are extra dependencies (I have just recently built my OS with centOS 8) or if there may be a certain step I may be missing?

running CTFFIND4 on tilted data

Dear All,

Is there any special precaution (e.g. switching on a particular flag) which we have to take while running CTFFIND4 on tilted data. We had preferential orientation problem so we tilted the stage to 20 and 30 degrees.

Any comments or suggestions regarding processing are welcome too!

Cheers,
Shabih

Error compiling version 4.1.13 on Linux - missing pdb.h & water.h files

I am trying to compile from ctffind-4.1.13.tar.gz (on Centos 7) but getting error of
missing include files pdb.h & water.h:
  tar -xf ctffind-4.1.13.targz
  cd ctffind-4.1.13
  ./configure
  make
   ...
  compilation terminated.
   In file included from src/core/symmetry_matrix.cpp:1:0:
   src/core/core_headers.h:98:17: fatal error: pdb.h: No such file or
directory
   #include "pdb.h"

Should I be installing some other dependencies or have these include files been simply 
excluded from the source code ?

Forum topic test

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