Re: [Pytom-mail] FRMAlignment - New

[Dustin M. <dus...@gm...>]

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
> 
> 
>