ctffind & ctftilt

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   **

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).

Hi all,

I updated my ctffind4 installation from veriosn 4.1.4 to version 4.1.13. Using the same parameters as before the update, I now get worse defocus estimations.

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?

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

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 ?

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Installed RELION2.1 from Github, tried with CTFFIND4.1.10 first the binary then compiled from source (got intel-mkl, wxWidgets etc.) installed in /usr/local/bin

Running through the RELION2.1 tutorial, used unblur/summovie for motion correction. I get stuck at CTF estimation, using all parameters from the manual the job runs but looks like it doesn't find the images. Contents of run.out is:
Using CTFFIND executable in: /usr/local/bin/ctffind
to estimate CTF parameters for the following micrographs:
*
*
...
*

We would like to embed the experimental camera image into a larger array. We would like to do this for two reasons:

1) To provide margin for image shifts so that the camera image does not intrude on itself (cyclic copy) when shifted.

2) To speed up FFT by using power of 2 algorithm.

For the K2 camera, this would be a 4096 x 4096 image for normal resolution and 8192 x 8192 for super-resolution.

I have problems finding the right routines for doing this in cistem. Such an extension would definitely be useful, if it doesn't already exist in the code. How should I proceed?

Hello,

I am trying to use Relion-2.1-beta-1 and CTFFIND4.1.8 however, I keep getting the following error: "WARNING: skipping, since cannot get CTF values for Micrographs/mic000001.mrc" for every micrograph. An empty micrographs_ctf.star file is generated.

The note.txt file reads
"++++ Executing new job on Mon Mar 19 18:49:23 2018
++++ with the following command(s):