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CCPEM  June 2018

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Subject:

Re: Experiment::divideParticlesInRandomHalves: some random subset values are zero and others are not.

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Fri, 1 Jun 2018 09:23:51 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (87 lines)

Yes, that makes sense: in most reported cases these things are a result of
errors in scripting.
Best,
Sjors

> Hi Sjors,
>
>     thanks a lot for this explanation! I finally realized that the data
> set had been generated by a script using the older metadata set of
> relion-1.4 and that I had put the wrong header (referring to additional
> metadata used in relion-2.1). So, data referred to in the header were
> missing! Upon removing the corresponding lines in the header it now runs
> smoothly and the metadata and metadata labels were added back. Have to
> see whether the result makes sense :-).
>
> BW, Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail: [log in to unmask]
> ------------------------------------------------------------------------
>
> Am 29.05.2018 um 19:23 schrieb Sjors Scheres:
>> Hi Dieter,
>>
>> Some particles were already used in a 3D refinement job earlier, and
>> hence have been assigned a random subset of 1 or 2. Other particles have
>> apparently been added in later and do not have a random subset. The
>> refine program (which uses rlnRandomSubset, the reconstruct doesn't)
>> complains about this, basically as a protection against not doing what
>> you would want to do (which is keep random half-sets always the same).
>> If you know what you are doing, you could just randomly assign 1 or 2 to
>> the particles that currently have a 0 in that column.
>>
>> HTH,
>>
>> Sjors
>>
>>
>>
>> On 05/28/2018 01:52 PM, Dieter Blaas wrote:
>>> Dear colleagues,
>>>
>>>      running 3D auto-refine with Relion-2.1 I get the below error:
>>>
>>> ERROR:
>>> ERROR Experiment::divideParticlesInRandomHalves: some random subset
>>> values are zero and others are not. They should all be zero, or all
>>> bigger than zero!
>>> File: /opt/relion/src/exp_model.cpp line: 207
>>>
>>> However, when running the same dataset with relion_reconstruct it runs
>>> to completion without any error. What might be wrong?
>>>
>>> Thanks, Dieter
>>>
>>> ------------------------------------------------------------------------
>>> Dieter Blaas,
>>> Max F. Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Fax: 0043 1 4277 9616,
>>> e-mail: [log in to unmask]
>>> ------------------------------------------------------------------------
>


-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres

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