Hi, data_particles works and particle extraction proceeds, thanks.

However, it turns out that relion_convert_star and also 
relion_star_handler both cut the input 3.0 star file, leaving only 1800 
particles in out of 3600.

Looking at the original 3.0 star file, there is nothing wrong at the 
cut-off point.

What could be the reason?

During conversion relion puts out "The input is a micrograph STAR file 
with CTF information", but there should not be a limit on number of 
micrographs?

Many thanks!

Leonid

Prof. Leonid Sazanov FRS
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria

Phone: +43 2243 9000 3026
E-mail: [log in to unmask]

On 17.11.20 22:10, Takanori Nakane wrote:
> Hi,
>
> > your star-files say "data_micrographs" instead of "data_particles", 
> might this be the problem?
>
> Possibly. In addition, you might have to add rlnOriginXAngst and 
> rlnOriginYAngst columns
> (all values can be 0).
>
> >> For tilted micrographs, I recommend Warp or SIMPLE 3.0. Both can write
> >> STAR files compatible with RELION.
> >
> > Are those compatible with 3.1?
>
> SIMPLE 3.0: Yes.
>
> Warp might write particles in the 3.0 format but conversion should be 
> straightforward.
>
> >      Also, we really like to use Topaz + Relion autopicks jointly 
> (after
> >      removing duplicates) to optimise picking.
>
> The Topaz wrapper script in the released version does not work well 
> when your images are
> scattered in several sub-directories. A fix is in 
> https://github.com/tbepler/topaz/issues/56.
>
> RELION 3.2 (not public yet) will have build-in Topaz integration.
>
> Best regards,
>
> Takanori Nakane
>
> On 2020/11/17 19:36, Hunkeler, Moritz wrote:
>> Hi,
>>
>> your star-files say "data_micrographs" instead of "data_particles", 
>> might this be the problem?
>>
>> Best,
>> Moritz
>>
>> On 11/17/20, 14:01, "Collaborative Computational Project in Electron 
>> cryo-Microscopy on behalf of Leonid Sazanov" <[log in to unmask] on 
>> behalf of [log in to unmask]> wrote:
>>
>>              External Email - Use Caution
>>
>>      Hi,
>>
>>      I tried both as produced by relion_convert:
>>
>>
>>      # version 30001
>>
>>      data_optics
>>
>>      loop_
>>      _rlnOpticsGroup #1
>>      _rlnOpticsGroupName #2
>>      _rlnAmplitudeContrast #3
>>      _rlnSphericalAberration #4
>>      _rlnVoltage #5
>>      _rlnMicrographPixelSize #6
>>      _rlnMicrographOriginalPixelSize #7
>>                  1 opticsGroup1     0.100000     2.700000 300.000000
>>      0.840000     0.840000
>>
>>
>>      # version 30001
>>
>>      data_micrographs
>>
>>      loop_
>>      _rlnMicrographName #1
>>      _rlnCoordinateX #2
>>      _rlnCoordinateY #3
>>      _rlnDefocusU #4
>>      _rlnDefocusV #5
>>      _rlnDefocusAngle #6
>>      _rlnCtfFigureOfMerit #7
>>      _rlnAutopickFigureOfMerit #8
>>      _rlnPhaseShift #9
>>      _rlnOpticsGroup #10
>> Motioncorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      119.000000  3939.000000 30563.130859 30813.681641 72.121552
>>      0.087226     0.624116     0.000000            1
>> Motioncorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      1035.000000  3962.000000 30547.072266 30797.623047 72.121552
>>      0.056962     0.585844     0.000000            1
>> Motioncorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      107.000000  3391.000000 30593.382812 30843.933594 72.121552
>>      0.079964     0.465404     0.000000            1
>> Motioncorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      2094.000000  2427.000000 31001.355469 31251.906250 72.121552
>>      0.058114     0.398799     0.000000            1
>>
>>
>>      and also replacing the optics part with the one from 
>> micrographs.star:
>>
>>
>>      # version 30001
>>
>>      data_optics
>>
>>      loop_
>>      _rlnOpticsGroupName #1
>>      _rlnOpticsGroup #2
>>      _rlnMtfFileName #3
>>      _rlnMicrographOriginalPixelSize #4
>>      _rlnVoltage #5
>>      _rlnSphericalAberration #6
>>      _rlnAmplitudeContrast #7
>>      _rlnMicrographPixelSize #8
>>      opticsGroup1            1 ../../Qsub/mtf_K3_300kV.star 0.420000
>>      300.000000     2.700000     0.100000     0.840000
>>
>>
>>      # version 30001
>>
>>      data_micrographs
>>
>>      loop_
>>      _rlnMicrographName #1
>>      _rlnCoordinateX #2
>>      _rlnCoordinateY #3
>>      _rlnDefocusU #4
>>      _rlnDefocusV #5
>>      _rlnDefocusAngle #6
>>      _rlnCtfFigureOfMerit #7
>>      _rlnAutopickFigureOfMerit #8
>>      _rlnPhaseShift #9
>>      _rlnOpticsGroup #10
>> MotionCorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      119.000000  3939.000000 30563.130859 30813.681641 72.121552
>>      0.087226     0.624116     0.000000            1
>> MotionCorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      1035.000000  3962.000000 30547.072266 30797.623047 72.121552
>>      0.056962     0.585844     0.000000            1
>> MotionCorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      107.000000  3391.000000 30593.382812 30843.933594 72.121552
>>      0.079964     0.465404     0.000000            1
>> MotionCorr/job009/Micrographs/FoilHole_15353235_Data_15352608_15352610_20201015_145359_fractions.mrc
>>      2094.000000  2427.000000 31001.355469 31251.906250 72.121552
>>      0.058114     0.398799     0.000000            1
>>
>>
>>      Both give zero particles.
>>
>>
>>      > For tilted micrographs, I recommend Warp or SIMPLE 3.0. Both 
>> can write
>>      > STAR files compatible with RELION.
>>
>>
>>      Are those compatible with 3.1?
>>
>>      Also, we really like to use Topaz + Relion autopicks jointly (after
>>      removing duplicates) to optimise picking.
>>
>>      Thanks for your help!
>>
>>      Leonid
>>
>>
>>
>>      >
>>      > Best regards,
>>      >
>>      > Takanori Nakane
>>      >
>>      > On 2020/11/17 18:09, Leonid Sazanov wrote:
>>      >> Hi,
>>      >>
>>      >> We have been using gctf for local per-particle ctf 
>> determination on
>>      >> highly tilted carbon micrographs (this is necessary to get 
>> things
>>      >> going). Gctf creates .star files in older style and particle
>>      >> re-extraction with local defocus values worked fine in 
>> relion3.0.
>>      >> However, with 3.1,  after using relion_convert_star to get 
>> 3.1 style
>>      >> .star, which looks fine for 3.1, re-extraction does not work 
>> - there
>>      >> are no errors but zero particles. We can work around it by 
>> extracting
>>      >> in 3.0 and then going back to 3.1 but would be nice to get it 
>> to work
>>      >> in 3.1 directly. Was anything changed in extraction step 
>> itself in 3.1?
>>      >>
>>      >> Thanks!
>>      >> Leonid
>>      >>
>>      >> 
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