--XMAG in ctffind3 command from Relion-1.4

Submitted by NancyM on Mon, 2016-01-11 18:16

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ctffind & ctftilt

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:
`which relion_run_ctffind` --i "micrographs_inspected.star" --o "micrographs_ctf.star" --ctfWin -1 --CS 2.7 --HT 300 --AmpCnst 0.1 --XMAG 50794 --DStep 6.4 --Box 512 --ResMin 30 --ResMax 5 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 100 --ctffind_exe /progs/ctf-140609/ctffind3_mp.exe

Thx for any input!

P.S. Is "XMAG" "effective" magnification and just Dstep/(A/pix)? Not a value I need to be concerned with?

Alexis Mon, 2016-01-11 20:16

This is the expected relationship is:
psize = dstep / xmag

where psize is the image pixel size and dstep is the detector pixel size.

In your case, the numbers don't quite work out...
1.215 != 64000 / 50794

NancyM Tue, 2016-01-12 17:38

Yes, very sorry, my error in typing.

--XMAG = 52675. So the psize=dstep/xmag relationship works out.

Is it true then that XMAG is not expected to refer to the nominal magnification at which I collected (29Kx)?

Thank you for the reply!

NancyM Tue, 2016-01-12 20:23

Thanks! That reassurance makes it more fun to continue with the processing. :-)