Re: [scipion-users] [scipion] micelles density subtraction

[Juha H. <juh...@he...>]

Hi Dmitry,

Either Xmipp or RELION protocols can be used for this.  You can search for
them (CTRL+F) using keyword "subtract".  Both require a mask that defines
the part you want to subtract plus a map used for subtraction (for me it
works better if this map is not sharpened, e.g. comes from Relion
auto-refine, not PostProcess).

Also, just to avoid confusion: our LocalRec is a plugin for localized
reconstruction of subunits. It does not have its own protocol for partial
signal subtraction (it is also independent of cryosparc).

Best wishes,
Juha

On Wed, Jul 8, 2020 at 3:42 PM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear Carlos Oscar and all,
>
>
>
> So for the localrec I will need the cryosparc to be installed on my system
> additionally to the SCIPION, right?
>
> If so, are there any recommendations from SCIPION point of view how to
> install the cryosparc on CentOS 7?
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
> ------ Original Message ------
> From: "Carlos Oscar Sorzano" <co...@cn...>
> To: "Dmitry A. Semchonok" <sem...@gm...>; "
> sci...@li..." <sci...@li...>;
> "sc...@cn..." <sc...@cn...>
> Sent: 08-Jul-20 2:33:18 PM
> Subject: Re: [scipion] micelles density subtraction
>
> Hi Dmitry,
>
> my experience with the standard tools in Scipion to subtract the membrane
> was not good (not for Scipion, but for the tools underneath). The one I did
> not try was localrec, that may be able to help and recently they announced
> an update of the plugin. We are working on our own subtraction, but it is
> still not ready.
>
> Cheers, Carlos Oscar
> On 7/7/20 9:54 PM, Dmitry A. Semchonok wrote:
>
> Dear colleagues,
>
> I would like to ask how to subtract the micelles density around your
> membrane protein in the proper way?
>
> What are the steps?
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
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