ctffind & ctftilt

Hi, I noticed some rather unusual results after running ctffind4 v.4.0.10 on images previously processed by ctffind3.
ctffind4 consistently gives much much smaller astigmatism and also sometimes defocus values are rounded, i.e. 36000 / 36000; or 27000 / 27000 (see below). What could be the reasons for this and which results are more reliable? Parameters as set in Relion were the same for both runs except low resolution for ctffind4 was 30 A instead of 100.

Here are some values from ctffind4 runs:

Hi, I am trying to use ctffind4 in relion1.3 by adding parameters in GUI. I tried both ctffind-4.0.12-linux64-compat.tar.gz and ctffind-4.0.12-linux64.tar.gz.
I got some errors as below.
Any suggestion will be appreciated!
Thanks,
Lei

Hi,
I'd like to estimate defocus value for a serial images. how to use the batch mode for ctffind4

1st I tried this:

echo mrc/input.mrc output_diag.mrc 1.0 300 2.7 0.07 512 30 5 5000 50000 500 100 no | ctffind

and ctffind4 considers 'mrc/input.mrc output_diag.mrc 1.0 300 2.7 0.07 512 30 5 5000 50000 500 100 no' as a input file...

so it is not necessary to put this command in a loop

2nd I tried:

-------
It's OK now. I find a way.

Dear Alexis,

first of all thanks for all the work on ctffind.
However, I was now running into a problem using the newest version of ctffind. For almost all my micrographs, ctffind is not able to refine the ctf values. In version 4.0.7 it works and therefore there is quite a significant difference in the estimated ctf values. The output of the logfile is below. Also the image of the ctf estimation is looking weird, as there seem to be things left out (see attached image).

We collected some data from Krios which has updated EPU software
for Falcon II which outputs 32 Mb images instead of usual 64 Mb.
ctffind3 reports "Unknown format" for these images - is that a known issue?
Perhaps they will work with ctffind4? We had an issue of compiling ctffind4 for AMD so far.

Many thanks!
Leo

Hello, I recently installed ctffind4.0.7 and used it successfully from Relion1.3. Now, without any changes to the system, I get the following error (with 4.0.7 and 4.0.8). The images were converted from dm3 to mrc in em2em. Some help will be appreciated. Michael

Greetings,

I've ran several ctf estimation trials in relion 1.3 with ctffind4 and varying parameters. Most of the time ctf estimation ran to completion except whenever the minimum resolution was set to 27,28,29,30,31,33,34A. Values nearby, such as 25 and 35A, work.Cycles with 30A through 33A output several cycles of the errors shown below. Interestingly, at 27,28,29, and 34A there is only a single output of the error. For 34A, if the box is changed from 512 to 256 it runs to completion without error output.

"forrtl: error (73): floating divide by zero

I'm looking at the thon rings after CTF estimation using CTFFIND4 in RELION. The experimental thon rings match those estimated by CTFFIND4 well. However, there seems to be a streaking/blurring artifact at the intersection of all quadrants creating a cross through the image. What causes this artifact? Should these micrographs be excluded from further processing? (Micrographs collected from DED camera in movie mode)

I got error as
gimplification failed:
0 constant 0>
../core/program_instances.f90: In function ‘init’:
../core/program_instances.f90:117:0: internal compiler error: gimplification failed
allocate(character(len=len_trim(adjustl(wanted_program_name))) :: self%program_name)
^

../core/program_instances.f90:117:0: internal compiler error: Abort trap: 6
gfortran: internal compiler error: Abort trap: 6 (program f951)
make: *** [program_instances.o] Abort trap: 6
Any idea?
Xing Meng

Hi Alexis,

I see that the ctffind4 binary available to download is for intel processors. Do you have any hints as to the best way (the one most likely to work!) to compile cttfind4 on an AMD system?

Thanks in advance,

David Gallagher
--
Research Scientist
Bacterial Complex I Group
MRC Mitochondrial Biology Unit