Hi,
The command is as follows (in one line):
relion_flex_analyse
--data MultiBody/jobXXX/run_data.star
--model MultiBody/jobXXX/run_model.star
--bodies bodies.star
--o MultiBody/jobXXX/subtracted
--subtract
--keep_inside MaskCreate/jobXXX/mask.mrc
--ctf
There is also an MPI version (relion_flex_analyse_mpi).
In the mask specified in "keep_inside",
0 means 'remove' while 1 means 'keep'.
The mask does not necessarily have to coincide
with a body but have to be smooth enough.
If the remaining region is small, you can make the box smaller by
for example "--normalise_bg_radius 96 --boxsize 128" (both in pixels).
Note that the remaining particle is automatically re-centered.
You have to update your reference and mask before Refine3D.
(Necessary translation is written to the console)
Best regards,
Takanori Nakane
On 2019/03/05 17:37, Purdy, Michael D (mdp3w) wrote:
> Hi. I have a case that is similar to the splicesome example in Nakane et
> al. (https://elifesciences.org/articles/36861). I would like to follow
> up the first multi-body run with signal subtraction of 3 of 4 bodies for
> subsequent 3D classification and refinement of the remaining body.
> Takanori, will you elaborate on the procedure summarized here
> (particularly the relion_flex_analyse details):
>
> "...we then used the relion_flex_analyse program to subtract the other
> three bodies from all experimental particle images, and performed a
> focused 3D classification on the SF3b without alignments."
>
> Mike
>
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
|