Comments and questions about defocus determination with ctffind3 and ctftilt.
I've come across an apparent inconsistency in the implementation of the CTF between SPIDER and CTFFIND/ CTFTILT with respect to how amplitude contrast is dealt with. One of the pages in the documentation on 3D reconstruction ( http://www.wadsworth.org/spider_doc/spider/docs/techs/recon/mr.html ) describes doing CTF determination with CTFFIND and subsequently correcting the CTF with SPIDER so this type of inconsistency may be a problem.
I think the current version of CTFTILT is v.1.5. I'm currently using the versions v.1.2 and v.1.3 of CTFTILT that were included in different releases of image2000, the MRC image processing suite. I was wondering what new features and/ or bug fixes there have been between v.1.2 and v.1.3 and also what's new v.1.5 (apart from support on multiple processors which was added in v.1.5, I think),
William
We've run into some difficulties with using CTFTILT (and CTFFIND) with cryoEM images of single particles in ice. After CTF determination, CTFTILT outputs an image with the fitted CTF on the left and the power spectrum on the right and it ought to be possible to confirm that the CTF has been fitted correctly by seeing if the Thon rings in the two halves of the images match up. Unfortunately, the Thon rings appear to be invisible in the case of an entire dataset of single particle ice images.
Hi,
I have a new Macbook with (i5 quad core intel processor) and OS 10.6.7.
I have gfortran-4.5 and g95 compilers.
I tried to compile the latest ctffind (ctf_101203).
I get the following error:
gfortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE \
ctffind3.o iof.o ioc.o -o ctffind3.exe
ld: warning: in ctffind3.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in iof.o, file was built for i386 which is not the architecture being linked (x86_64)
Undefined symbols:
"_main", referenced from:
start in crt1.10.5.o
Dear Niko,
I have a small question regarding ctffind. Please find attached output from the program.
I'm actually interested in two things: should I change ResMax for better correlation between ctf fit and power spectrum and the second one is what are additional grey circles in ctf fit on top of the image?
Thank you in advance.
I am looking for a way to estimate CTF from average power spectrum.
This is a ridiculously trivial request, but I would like to suggest that the output format for the scan step size (variable DSTEP) be changed from F9.1 to F9.3. This would be lines 111 and 124 in ctffind3.f and ctftilt.f, respectively.
The latest version of ctftilt (ctf_100930.tar.gz) is producing segmentation faults. After a little bit of poking around and debugging I was able to trace the problem to an uninitialized variable RMSMIN.
The main program sets the value for RMSMIN at line 256
DO 71 I=J-1,1,-1
IF (BINS(I).LT.CMAX/10.0) THEN
RMSMIN=(I-1)*(MAX-MIN)/(NBIN-1)+MIN
GOTO 72
ENDIF
71 CONTINUE
Hi,
How does ctffind3 calculate the azimuthal angle? Is is calculated from the two ctf defocus values? We want to write ctf values from manual estimation into the xmipp files and do not know how to handle the value for the azimuthal angle!
Thanks a lot, Dieter
