ctffind & ctftilt

Hello all,

Should the input pixel size for ctffind when using the stretch-only anisotropic magnification correction parameters be that of the uncorrected input pixel size or should it be the pixel size after mag correction using stretch-only parameters?

As of now, I am assuming it is the nominal pixel size of the uncorrected input images, and then if the pixel size is changed during mag distortion correction in ctffind using stretch-only parameters, this is passed on to the rest of the program.

Thanks for your help!

Hello,

I was wondering if you might incorporate this new feature into future versions of CTFFind?

I think it would be a big aid if calling the program with something like -h/--h/-help/--help would output a full list of required and optional parameters and switches.

Currently in CTFFind 4.1.8 I receive this when I attempt that:

$ ./ctffind help
Usage: ctffind [--old-school-input] [--old-school-input-ctffind4] [--amplitude-spectrum-input] [--filtered-amplitude-spectrum-input] [--fast] [controller_address] [controller_port] [job_code]

Hey there,

I am using CTFFIND4.1.8 in Relion 2.1b1 on MotionCor2 corrected micrographs, Apix is 1.43 (73k Mag and detector pix size is 14um). I have noticed the --XMAG flag is not update and the --DStep is taking the Apix:

`which relion_run_ctffind_mpi` --i ./MotionCorr/job002/corrected_micrographs.star --o CtfFind/job038/ --CS 2.7 --HT 200 --AmpCnst 0.07 --XMAG 10000 --DStep 1.43 --Box 512 --ResMin 28 --ResMax 4 --dFMin 5000 --dFMax 35000 --FStep 500 --dAst 100 --use_noDW --ctffind_exe /home/[...]/ctffind-4.1.8/bin/ctffind --ctfWin 4090 --is_ctffind4

What am I missing?

Hi all,

I did not have color in my pdf... But in the script it is ok... I can put on color with AI by using .ps file. I haven't tried in Linux system yet...

Here is the plot:

Many thanks for the helping!

Hong

Hihi,

I am a new user and try to use ctffind to get its output for NovaCTF. It was fun when I used a dataset has 2048 x 2048, but when it ran on my dataset, it returned error: Segmentation fault 11. And my dataset dimension is 3710 x 3838, it contains 104 micrographs.

Here is the header of my stack:

Map mode .............................. 6 (unsigned 16-bit integer)
Start cols, rows, sects, grid x,y,z ... 0 0 0 1 1 1
Pixel spacing (Angstroms).............. 5.600 5.600 5.600

Hi

I downloaded ctffind-4.1.8 from authorised webpage (http://grigoriefflab.janelia.org/ctf) and tried to install using the instruction from installation manuial i.e. the shell command `./configure && make && make install'
should configure, build, and install this package. However it stops with the following error:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes

Hi, there are some problems when I used ctffind4.1 in relion. ctffind4.1 was the version of ctffind-4.1.8-linux64.tar.gz

../../Relion-beta/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory
../../Relion-beta/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory
../../Relion-beta/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory

Hi,

With large (and fairly sparse) particles such as RyRs, I often find that I have strong Thon rings at low to medium resolution (presumambly from the protein), and then nice Thon rings at ~3-4 Å (from the solvent). This is particularly evident when processing using movie frames as input. (see example attached).

CTFFIND does a pretty good job of fitting both, but I wonder in such a case whether there might be some benefit in using discontinous resolution ranges for the CTF fit - e.g. 20-6Å for the protein, and 4-3 Å for the solvent?

Cheers
Oli

Want to download ctffind4, but can't find a "download" button anywhere on http://grigoriefflab.janelia.org/ctffind4
What am I doing wrong?
-Fred Sigworth

Dear Niko, dear Alexis and all,