Re: [Pytom-mail] FRMAlignment - New

[Benjamin H. <him...@gm...>]

Hi Dustin,

If your pixel size is 2nm as you have stated, your Nyquist limit is 4nm,
and the returned resolution is 4.04 nm - It probably has to do with this
more so than the wedge masking, is your pixel size entered correctly? Even
if the particles have been aligned falsely to have their missing wedge
coincide, this shouldn't inflate the FSC because it is a normalized metric.

-Ben H.

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On Sat, Feb 20, 2016 at 3:04 PM, Dustin Morado <dus...@gm...>
wrote:

> Ok I’ll try setting the missing wedge to empty (0,0?). I am pretty sure my
> wedge info is correct. Here is a single particle from the list:
>
> <Particle Filename="Particles/tomogram_00067_000014.em">
>   <Rotation Paradigm="ZXZ" X="159.572727907" Z1="357.684564976"
> Z2="266.804752529"/>
>   <Shift X="-4.54808395912" Y="-5.45043039396" Z="-1.90781399571"/>
>   <PickPosition Origin="../../TOMOS/tomogram_00067.mrc" X="220.0"
> Y=“554.0" Z="406.0"/>
>   <Wedge Type="SingleTiltWedge">
>     <SingleTiltWedge Angle1="30.0" Angle2="30.0" CutoffRadius="0.0"
> Smooth="0.0">
>       <TiltAxisRotation Z1="0.0" Z2="0.0" X="0.0"/>
>     </SingleTiltWedge>
>   </Wedge>
>   <Score RemoveAutocorr="False" Type="FRMScore" Value="0.301624138979">
>     <PeakPrior Filename="" Radius="0.0" Smooth="-1.0"/>
>   </Score>
>   <Class Name="1"/>
> </Particle>
>
> and the data was collected from -60, 60 at 3 degrees increments.
>
> —
> Cheers,
> Dustin
>
>
> > On Feb 20, 2016, at 4:44 AM, Yuxiang Chen <che...@gm...> wrote:
> >
> > Hi Dustin,
> >
> > that means for some reason the determined resolution (according to the
> set FSC value) is too high, which cannot be true.
> > Most likely the particles were aligned to the missing wedges. Please
> check the wedge settings in your particles.
> > If the wedges are set correctly and the problem still occurs, I'd
> suggest to set the wedges to empty to avoid aligning towards missing wedge
> direction.
> >
> > Cheers,
> > Yuxiang
> >
> >
> >
> > On Sat, Feb 20, 2016 at 2:47 AM, Dustin Morado <dus...@gm...>
> wrote:
> > Hi all,
> >
> > I keep getting the following termination to my FRM jobs
> >
> > current resolution 40.4014545455 1.03125
> > New frequency too high. Terminate!
> >
> > My Job field has the following:
> > <FRMJob PeakOffset="4" BandwidthRange="[4, 32]" Frequency="6"
> Destination="." MaxIterations="10" RScore="False" WeightedAverage="False"
> BFactor="None" AdaptiveResolution="0.1" FSC="0.5”>
> >
> > My particles are 64x64x64 with a 2nm pixel size so for some reason even
> if I set the initial frequency to an incredibly low resolution I still get
> this same abort. I have tried changing the frequency and the bw_range, but
> the only way I can get it to run for more than one iteration is to set the
> FSC to a very high value ~0.75+.
> >
> > Any suggestions?
> >
> > —
> > Cheers,
> > Dustin
> >
> >
> >
>
>
>
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