ctffind & ctftilt

Hi all,
I am currently using CTFTILT on a set of micrographs taken at a -60 tilt angle. The TLTANGLE output consists of only positive values. This is confusing as someone else in my lab was able to get the correct angle sign from the older CTFTILT version. Due to the high tilt angle, my micrographs are not of very high quality, and I am struggling with getting the program to work on a majority of the micrographs. Any suggestions would be greatly appreciated!
Thanks,
Vu

Hi,
as in my first post in the signature user group I first want to thank the developers for making available this fantastic software!

Hi Niko

I'm a PhD working with Corinne Smith at Warwick.

I have been using ctftilt for a while now but have run into a problem with a new tilt series. This series was recorded at 57252x mag (with 1.43x correction due to the CCD position) at ~42 degrees tilt (as far as we can go) using the following parameters:

1.4,200.0,0.15,57252,15.0,1
128,200.0,5.0,5000.0,30000.0,1000.0

The images are 4096x4096 TIFF format converted MRC images (converted using tif2mrc).

Is there a program, other than frealign, to CTF correct (amplitudes or just phase flipping) a single image using the values obtained from ctffind3 (i.e. correction taking into account some astigmatism). I have a few programs that correct CTF on single images but they all assume no astigmatism.

Thanks

Hello Niko,
I compiled the mp version of ctffind3.f, showing no any compiling error.
When starting running, it produced 'segmentation fault' and aborted.
Thanks

Xing Meng

Hi
my questions are regarding conversion between the values from CTFFIND to the ones that I should use for TF C (CTF correction)in Spider,

first, if I understand correctly I should use the average of DFM1 and DFM2 as the defocus value

but then,
should I use the value of the following difference as astigmatism?

(DFM2 - DFM1)

or should I use (DFM2 - average)

according to TF C command in SPIDER the astigmatism is :

Hello Niko,

Are the parameters written in ctftilt.com the optimum ones? And is there different optimums for, lets say film at 60 000x and 4k ccd at 100 000x? Or is it actually not so useful for a ccd data collection where the recorded area is much smaller?
in particular, I am not sure what TiltA and TiltR are.

By advance, thank you.

original parameters:
128,200.0,8.0,5000.0,30000.0,1000.0,0.0,2.5
!Box,ResMin[A],ResMax[A],dFMin[A],dFMax[A],FStep[A],TiltA[deg],TiltR[deg]

Parameters that I've put in today for film data at 60 000x. :

Hello Niko,

Using a fairly high mag (59 000 on film) my Nyquist frequency is 2.4 Å. To calculate the defocus value, the info between 2.4 Å and ~5 Å is more detrimental than useful. I see that you can limit the estimation to a certain resolution range. But is it possible to actually reduce the image size by a factor of two so that I get a better signal and better sampling in the useful range and a speedup of a factor of 4 in computing time?
Is it a good thing to do? or would bad things happen if I do it that way? Maybe it's an option that I didn't see..

By advance, many thanks.

hello,

i am trying to compile ctffind on mac (snow leopard 10.6.2), and i am having a small problem.
the problem is with compiling ioc.c with gcc - it gets compiled, but then when trying to put it
all together, there is a following error:

gfortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE \
ctffind3.o iof.f ioc.o -o ctffind3.exe
ld: warning: in ioc.o, file is not of required architecture

i tried to change the compilation option in gcc to -mtune=generic, and tried with different
types, but the result is always the same.
any idea what i could do ?

best,

jp

Hi Niko,

am currently testing version 3.2 and 3.3 of ctffind3.

Interestingly, when I use the same images to determine defoci/ang parameters with both version, I do get different output values in both, defoci and ang.
Also, the output image from version 3.2 shows crisp Thon rings ... compared to the output form the newer version. Is there any post-processing done with the output image ? Can you let me know, what has changed going from version 3.2 to 3.3 and whether the parameters obtained from the previous verions are still valid ?

Best,
-T.

V 3.2