[3dem] Floating fsc

Benjamin Himes himes.benjamin at gmail.com
Fri Nov 2 15:06:19 PDT 2018


Hi Steinar,

I will give a +1 to Vladan's suggestion. In emClarity, the option
"fscSplitOnTomos" was added for just this reason.

I realize you have removed the overlapping particles, by editing your star
files I suppose, but what distance do you use to ensure no overlap?

Keep in mind that there may be mixing of signal/noise some distance outside
your particle envelope as well, especially if you are multiple micron off
focus.

Ben H



On Fri, Nov 2, 2018, 3:00 PM <3dem-request at ncmir.ucsd.edu> wrote:

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>    1. Re: Add random noise to reconstruction (Vladan Lucic)
>    2. Re: Add random noise to reconstruction (Steinar Halldorsson)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 2 Nov 2018 18:21:04 +0100
> From: Vladan Lucic <vladan at biochem.mpg.de>
> To: <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Add random noise to reconstruction
> Message-ID: <8b43672d-ec5e-c6ff-514d-bd06dc136257 at biochem.mpg.de>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi Stelnar,
>
>
> Perhaps you have double (overlapping) particles, as a result of double
> picking or translations during refinement for example. A quick way to
> check for this is to make particle half-sets from different tomograms
> (split tomograms in two groups and make each half particle set from one
> group). In this way, double particles will always be in the same
> particle half-set. If the FSC between these halves goes to 0, it's
> double particles.
>
>
> Just a guess, hope it helps
>
>
> Best,
>
> Vladan
>
>
> On 11/2/18 5:44 PM, Steinar Halldorsson wrote:
> >
> > Hi all
> >
> >
> > I have something which looks like an artefact in my FSC curves from
> > tomography data calculated in Relion. Basically the curves hover
> > around 0.1 instead of reaching 0... And this is not coming from my
> > mask btw. There is quite a lot of information (protein) outside of the
> > mask, you can see clear but slightly smeary density from neighbours in
> > the final maps, and I wonder if this is?causing these correlations?
> > One way I have thought to test this is to take my two half maps,
> > somehow add random noise to parts outside of my region of interest and
> > then recalculate my FSC.
> >
> >
> > Firstly, does this sound like a reasonable thing to try?
> > Secondly, does anyone have a suggestion of how to actually do the
> > random noise addition outside of my region of interest?
> >
> > Cheers,
> >
> > Steinar
> >
> >
> > ---
> >
> > Steinar Halldorsson
> >
> > Postdoctorate Fellow
> >
> > Rosenthal lab
> >
> > The Francis Crick Institute
> > London, United Kingdom
> >
> > The Francis Crick Institute Limited is a registered charity in England
> > and Wales no. 1140062 and a company registered in England and Wales
> > no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
> >
> >
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> Message: 2
> Date: Fri, 2 Nov 2018 18:19:11 +0000
> From: Steinar Halldorsson <steinar.halldorsson at crick.ac.uk>
> To: Vladan Lucic <vladan at biochem.mpg.de>, "3dem at ncmir.ucsd.edu"
>         <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Add random noise to reconstruction
> Message-ID:
>         <
> HE1PR03MB300415F5567827E4B12DF23ABFCF0 at HE1PR03MB3004.eurprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Vladan
>
>
> I have removed overlapping particles but it didn't change the FSC
> behaviour.
>
>
> Steinar
>
> ________________________________
> From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Vladan Lucic <
> vladan at biochem.mpg.de>
> Sent: 02 November 2018 17:21:04
> To: 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] Add random noise to reconstruction
>
>
> Hi Stelnar,
>
>
> Perhaps you have double (overlapping) particles, as a result of double
> picking or translations during refinement for example. A quick way to check
> for this is to make particle half-sets from different tomograms (split
> tomograms in two groups and make each half particle set from one group). In
> this way, double particles will always be in the same particle half-set. If
> the FSC between these halves goes to 0, it's double particles.
>
>
> Just a guess, hope it helps
>
>
> Best,
>
> Vladan
>
>
> On 11/2/18 5:44 PM, Steinar Halldorsson wrote:
>
> Hi all
>
>
> I have something which looks like an artefact in my FSC curves from
> tomography data calculated in Relion. Basically the curves hover around 0.1
> instead of reaching 0... And this is not coming from my mask btw. There is
> quite a lot of information (protein) outside of the mask, you can see clear
> but slightly smeary density from neighbours in the final maps, and I wonder
> if this is causing these correlations? One way I have thought to test this
> is to take my two half maps, somehow add random noise to parts outside of
> my region of interest and then recalculate my FSC.
>
> Firstly, does this sound like a reasonable thing to try?
> Secondly, does anyone have a suggestion of how to actually do the random
> noise addition outside of my region of interest?
>
> Cheers,
>
> Steinar
>
>
> ---
>
> Steinar Halldorsson
>
> Postdoctorate Fellow
>
> Rosenthal lab
>
> The Francis Crick Institute
> London, United Kingdom
>
> The Francis Crick Institute Limited is a registered charity in England and
> Wales no. 1140062 and a company registered in England and Wales no.
> 06885462, with its registered office at 1 Midland Road London NW1 1AT
>
>
>
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>
>
>
> The Francis Crick Institute Limited is a registered charity in England and
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> 06885462, with its registered office at 1 Midland Road London NW1 1AT
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