But from an unmasked (or whole-particle mask) Refine3D run, or from a run with a mask around the region to be kept? I have found the latter better in the limited experience I have with it, but still unsure which is better in theory.
Cheers
Oli
On 8/9/17, 7:36 AM, "Collaborative Computational Project in Electron cryo-Microscopy on behalf of Sjors Scheres" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Hi Reza,
From Refine3D, or from postprocessing without sharpening. The data is
not sharpened, so never subtract with sharpened maps. We normally just
use the map from Refine3D.
HTH,
Sjors
On 08/09/2017 12:26 PM, Reza Khayat wrote:
> Hi,
>
> For the signal/density subtraction analysis, is it best to subtract the final reconstruction from Refine3D or postprocessing?
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
>
> ________________________________________
> From: Collaborative Computational Project in Electron cryo-Microscopy [[log in to unmask]] on behalf of Christopher Browning [[log in to unmask]]
> Sent: Wednesday, August 9, 2017 4:15 AM
> To: [log in to unmask]
> Subject: [ccpem] e2boxer21.py
>
> Hi,
>
> I've been trying out different particle boxing programs and came across e2boxer21.py within the EMAN2 gui. I've started using it and noticed that one can use 2D or 3D references to box the particles. I've imported a 3D reconstruction I have and used that to box partiles but can someone explain me a bit more how this works because it doesn't seem to be boxing the right things.
>
> Many Thanks,
>
> Chris
>
>
> This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.
--
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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