Tilt angle output from CTFTILT

Submitted by Vu on Thu, 2010-09-23 19:00

Forums

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

niko Thu, 2010-09-23 19:51

Could you please post the input parameters you are using (all the number on the two lines with parameters)?

Vu Fri, 2010-09-24 19:28

These are the parameters that I used:
6.2,120,0.15,42000,15,2
128,30,10,10000,30000,1000,60,2
I used similar parameters for micrographs taken at +30 deg tilt and obtained good results. I also tried -60 as the tilt angle but the output was still positive.
Thanks for your help!

niko Fri, 2010-09-24 21:41

The parameters look OK. If I understand you correctly, ctftilt determines a tilt angle of 60 deg but you were hoping to get a -60 deg angle. For any particular tilt there are two possible solutions ctftilt can find. They have opposite signs for the tilt angles and tilt axes. A tilt by +60 deg and an angle alpha for the tilt axis is the same tilt as a tilt of -60 deg and alpha + 180 (NOT -alpha, as I wrote here before) for the tilt axis. Which one is picked by ctftilt should be more or less random.

If the tilt angle is not determined correctly, you can also play with the resolution limits. For example, you can change 30 to 50 or 100 and see if the results improve. The resolution range sometimes has to be tuned a bit for optimal performance.

Grigory Mon, 2012-05-28 13:54

Hello Niko,

I ran last ctftilt version on my +45 tilted data and get values for tilt angle and tilt axis. Tilt angle seems to be around expected 45 deg. and the sign is more or less random. If I used previous versions of CTFTILT I would correct the sign of tilt angle and tilt axis also.

On the website you posted that in version 1.7 tilt angle is changed by *(-1). I wonder if this affects tilt axis angle? Which sign should I apply for it?

niko Tue, 2012-05-29 08:15

It is correct that the tilt axis in previous versions was not limited to a particular range. Now it is limited to be between 90 and -90 deg. This should not change the overall meaning of the determined tilt geometry. A tilt axis outside the range of +-90 deg can always be converted into a tilt axis within +-90 deg bu adding or subtracting 180 deg and changing the sign of the tilt angle. The meaning of the tilt axis has not changed in the new version, its value is simply limited to be within +-90 deg. The only change concerns the meaning of the tilt axis which is now the negative of what it was before.

Grigory Thu, 2012-05-31 10:26

Dear Niko,

thanks for your reply, but probably I was not clear:
I have +45-tilted and -45-tilted images. From ctffind v2.7 for most of the micrographs I got expected tilt angle sign (around + or - 45),but some of them shows the opposite sign (-45 instead of expected +45 and vice versa), e.g:

tltaxis=-81.18, tangle=-46.86 for -45 (1)
tltaxis=86.83,  tangle=-43.35 for +45 (2)

My question is if I should change the sign of "wrong" tangle (2) as well as corresponding tltaxis?

niko Thu, 2012-05-31 11:59

If ctftilt fails in finding the correct tilt geometry you should not use the values at all, of course. If you think that ctftilt found the right tilt geometry but, according to your own conventions, tangle should have the opposite sign, you can convert the values found by ctftilt by calculating

tltaxis_new = tltaxis_old + 180
tangle_new  = -tangle_old

So in your example above:

tltaxis_new = 86.83 + 180 = 266.83
tangle_new  = 43.35

This transformation should not change the tilt geometry, i.e. the actual defocus values calculated at the particle coordinates should remain unchanged.

Grigory Fri, 2012-06-01 18:36

Niko, one more question about your last post: earlier you wrote that "A tilt by +60 deg and an angle alpha for the tilt axis is the same tilt as a tilt of -60 deg and -alpha for the tilt axis. Which one is picked by ctftilt should be more or less random."
Now you propose to correct the same error by changing tilt angle sign, but new "alpha"=alpha+180.

Is it just because convention changes in version 2.7?

niko Sat, 2012-06-02 01:17

Thanks for pointing this out. I now see that my earlier post from 2010-09-24 was wrong. You need to change the sign of the tilt angle and add or subtract 180 from the tilt axis. Sorry about this error! What I wrote on 2012-05-31 is correct.