Hi,
>> If so, did you use an absolute path in the link?
>
> ...but not absolute. Is this a requirement?
>
> To be clear, the file organization is:
>
> RelionProject -- CtfFind
> -- default_pipeline.star
> -- Import
> -- ManualPick
> -- Select
> -- Micrographs -- linkname1.mrc -> ../../data/actualfile1.mrc
> linkname2.mrc -> ../../data/actualfile2.mrc
>
> Perhaps I should make absolute links to the actual Falcon3 MRC files?
Yes, please try linking by absolute paths.
Best regards,
Takanori Nakane
> Thanks again,
>
> James Conway
> ----------------------------------------------------------------------
> James Conway, PhD.,
> Professor, Department of Structural Biology
> Director, Molecular Biophysics and Structural Biology Graduate Program
> University of Pittsburgh School of Medicine
> Biomedical Science Tower 3, Room 2047
> 3501 5th Ave
> Pittsburgh, PA 15213
> U.S.A.
> Phone: +1-412-383-9847
> Fax: +1-412-648-8998
> Email: [log in to unmask] <mailto:[log in to unmask]>
> Web: http://www.structbio.pitt.edu/index.php/12-faculty/18-james-conway
> ----------------------------------------------------------------------
>
>
>
>> On 2019/08/24 16:31, James Conway wrote:
>>> Perhaps a trivial error, but I haven't found it described here. I
>>> have done the following:
>>> 1. Imported non-movie Falcon3 micrographs from EPU 2.3 into Relion 3.0
>>> 2. Run CTF Estimation (CTFFIND-4.1)
>>> 3. Rejected the worst 25% using Subset selection and rlnCtfMaxResolution
>>> Now I am attempting a manual pick of a subset of micrographs to get
>>> started. The Manual Picking fails with (run.err):
>>> terminate called after throwing an instance of 'std::out_of_range'
>>> what(): basic_string::substr
>>> The other output (run,out) is:
>>> Setting angpix to 1.04 based on the input STAR file...
>>> Set low-pass filter to 20 due to downscaling of 0.2
>>> Saved ManualPick/job004/micrographs_selected.star
>>> The saved micrographs_selected.star has micrographs listed but, of
>>> course, no picked particle locations.
>>> The command generated by the GUI is:
>>> `which relion_manualpick` --i Select/job003/micrographs.star --odir
>>> ManualPick/job004/ --pickname manualpick --allow_save --fast_save
>>> --selection ManualPick/job004/micrographs_selected.star --scale 0.2
>>> --sigma_contrast 3 --black 0 --white 0 --lowpass 20 --ctf_scale 1
>>> --particle_diameter 740 >> ManualPick/job004/run.out 2>>
>>> ManualPick/job004/run.err
>>> Note: The particle diameter is large because these are bacteriophage
>>> capsids - I expect to extract images with a sizable bin-factor to
>>> start with.
>>> I don't know how to troubleshoot this further - the error message is
>>> not very specific about the parameter that is out of range. I can't
>>> see any obvious fault with the input data or the parameters.
>>> Thanks for any insights.
>>> James Conway
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