ctffind & ctftilt

Dear Alexis,

Dear Alexis,

Do I have to include "/lmb/home/tmartin/programs/ctffind-4.0.9-linux64/ctffind --omp-num-threads 1 --old-school-input" in relion1.4 gui to run the ctffind4 or is it meant only for compatibility with relion1.3?

Thanks.

Regards,
Shabih

Hello, I am using CTFFIND 4.0.17 along with Relion 1.4. Whenever I try to run ctffind, it starts, prints "SEARCHING CTF PARAMETERS...", and then gives this
>forrtl: error (65): floating invalid
Image PC Routine Line Source
ctffind 00000000016B81B9 Unknown Unknown Unknown
ctffind 00000000016B6B30 Unknown Unknown Unknown
ctffind 00000000015D85D2 Unknown Unknown Unknown
ctffind 0000000001578928 Unknown Unknown Unknown

Hi,

I'm getting very poor CC values (in both the txt files) when using ctffind-4.0.17. The CC values for ctffind-4.0.7 are much better; however, the generated power spectrum from ctffind-4.0.17 matches the micrograph much better than ctffind-4.0.7. I would appreciate any suggestions.

I am running ctffind3 from Relion-1.4. My calibrated pixel size at the specimen level is 1.215 A/pix. I collected on a DE-20 (6.4um physical pixel size) at a nominal magnification of 29,000x. A/pix is given as input to Relion and --DStep 6.4 is given as a ctffind3 argument. On printing the command, --XMAG is filled as 50794. Question: How is --XMAG populated in the ctffind3 command and what exactly does it represent? Do I need to manually change this to my nominal 29,000x? Below is an example of a ctffind3 command I would run in Relion-1.4:

[meyerna@MRBA648 Relion]$ *** The command is:

Hi,

On our Linux system, we found that the ctffind_plot_results.sh always give the same result.
Then found that /tmp/tmp.pdf is written by someone else and cannot be overwritten.

Probably it is better to modify the script as follows:

pdftk /tmp/tmp.pdf update_info /tmp/pdftemp.txt output $output_fn
rm /tmp/tmp.pdf # remove the temporary /tmp/tmp.pdf file.

Thanks.

Hi, I am using ctffind4 version 4.0.16 in Relion-1.4:

"/home/donghuac/ctffind --omp-num-threads 1 --old-school-input"

But still got the following error:

Estimating CTF parameters using Niko Grigorieff's CTFFIND ...
6.68/6.68 min ............................................................~~(,_,">
ERROR: cannot find line with Final values in Micrographs/12102015stack0004_ctffind3.log
File: src/ctffind_runner.cpp line: 299
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

I have been running ctffind4 in parallel on a number of micrographs, and have noticed that a large number of micrographs do not have output from ctffind4, indicating it either did not finish, or did not produce output.

When I do this on several hundred micrographs at once, it complains about a temporary .CTFFIND file having already been deleted in some instances.

CTFFIND finishes normally on more of the micrographs when I execute fewer jobs, but appears to always fail on a subset.

Hi,

I am getting a seg-fault on certain micrographs from a series of tilted images collected on K2. All micrographs are 3710x3838 from K2 and tilted. Certain micrographs work, however others seg-fault. I have not been able to systematically track down why some work and others do not. Image mins, maxs, means, and stdevs are all similar. Nominal defocus values are standard (1-2 microns). Tilt angles are all 30° for this set.

I am using the latest version of CTFTilt.

Hi all,

CTFFIND4 has been working wonderfully for us, many thanks for its development and support!

I was just wondering whether it might be worth at some point adding in an option to flag (or discard) images with crystalline ice? This is typically very obvious in the power spectrum, and I guess all that info is in the *_avrot.txt files... this would be very handy when analyzing large datasets for directly getting rid of these micrographs without having to visually inspect them (or at least to flag them for inspection).