Hi Simona,
You probably don't need to worry about it, provided you have come all
the way through the RELION pipeline. The refine program writes out which
angpix value it will use in its model.star files.
HTH,
Sjors
On 03/22/2018 09:43 AM, Simona Pilotto wrote:
> Dear Sjors,
>
> thank you for the info. Based on that, do you mean that I have to
> check the other flags (and parameters on the command line) to
> understand if they are correct or not or that I don't need to care
> about that? I am sure that in both cases ctf and defocus are correct
> because the Thon rings are correct, I am just wondering if relion will
> use those flags for processing and how much they can affect the results.
>
> Regards
> Simona
>
>
>
> 2018-03-21 11:02 GMT+01:00 Sjors Scheres <[log in to unmask]
> <mailto:[log in to unmask]>>:
>
> Hi Simona,
>
> This is a bit of history I'm afraid. The only thing that matters
> is the
> ratio between *rlnDetectorPixelSize* and *rlnMagnification* which
> together define the Angpix. In some procedures, rlnMagnification
> is set
> to 10000, so that rlnDetectorPixelSize is actually in Angstroms/pixel.
>
> HTH,
>
> S
>
>
> On 03/21/2018 09:40 AM, Simona Pilotto wrote:
> > Dear EM community,
> >
> > I have a dubt about the info reported in the star files as
> > *rlnDetectorPixelSize* and I would like to understand the right
> > meaning of it.
> > In theory it should refer to the detector pixel size (as the name
> > suggests) but since I never gave this info during processing it
> can't
> > be this the right meaning.
> > The only parameter about pixel size I can give is the apix so I
> > suppose this is the real meaning of it.
> > Now, if it means apix I would like to understand why if I
> process data
> > with CTFfind this value is 1.06 (correct) and if I process with GCTF
> > this value becomes 14 (wrong).
> > I also checked the gctf1.out file and this is what I found:
> >
> > User input parameters:
> > --apix 1.060
> > --cs 2.70
> > --kv 300.00
> > --ac 0.10
> > --astm 100.00
> > --logsuffix _gctf.log
> > --gid 1
> >
> > All parameters to be used:
> > General options:
> > --apix 1.060
> > --dstep 14.000
> > --kv 300.00
> > --cs 2.70
> > --ac 0.10
> >
> > As you can see there is a parameter with this value but I don't know
> > if it is the same thing.
> > Now the question is how much this value can affect my processing and
> > how to correct it.
> >
> > Thank you for the help.
> >
> > Regards
> > Simona
> >
> >
> > --
> > PhD
> > Structural Biology group
> > Dept. of Biology and Biotechnology
> > University of Pavia
> > via Ferrata, 9/A
> > 27100 Pavia
> > Tel +39 (0)382 985534
> > web: www.unipv.it/biocry <http://www.unipv.it/biocry>
> <http://www.unipv.it/biocry>
>
> --
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061 <tel:%2B44%20%280%291223%20267061>
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
> <http://www2.mrc-lmb.cam.ac.uk/groups/scheres>
>
>
>
>
> --
> PhD
> Structural Biology group
> Dept. of Biology and Biotechnology
> University of Pavia
> via Ferrata, 9/A
> 27100 Pavia
> Tel +39 (0)382 985534
> web: www.unipv.it/biocry <http://www.unipv.it/biocry>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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