Thanks for coming back, Neil!
Excellent. I think that means there is no real problem here then.
Sjors
On 12/13/2017 04:31 PM, Neil Rzechorzek wrote:
> My apologies to followers of this thread, and in particular to Sjors
> and the rest of the Relion team.
>
> By a stroke of pure bad luck it looks like the issue at our end was as
> a result of a patch we had attempted to apply locally. We're running
> Relion2.1.b1 on a centrally-administered cluster and we have some
> system-specific challenges to deal with.
>
> Removing this patch does result in correct CTFfind output through the
> Relion GUI; in brief, we are now getting _rlnMicrographNameNoDW #1
> pointing to *_noDW.mrc, and _rlnMicrographName #2 pointing to *.mrc,
> as expected.
>
> Apologies if this added to the confusion!
>
> With kindest regards,
>
> Neil
>
>
> On 13/12/2017 16:08, Niks J wrote:
>> Thank you Sjors, Neil, Elad, Ambrose, John, Shawn and Munan for
>> replying.
>>
>> Since I am getting noDW.mrc and .mrc I will go with the Sjors and
>> Elad's suggestion. For some reason gui is giving error but still
>> making those conversions as evident by presence of noDW files.
>>
>>
>>
>> Best,
>> Nikhil
>>
>> On Wed, Dec 13, 2017 at 7:46 AM, Neil Rzechorzek <[log in to unmask]
>> <mailto:[log in to unmask]>> wrote:
>>
>> Apologies for re-raising this, but we have some confusion at our
>> end!
>>
>> Running Motioncor2.1.0.2 via the Relion2.1.b1 GUI with
>> dose-weighting switched on gives the following
>> correct_micrographs.star file arrangement:
>>
>> _rlnMicrographNameNoDW #1
>> _rlnMicrographName #2
>> MotionCorr/job008/Micrographs/*_noDW.mrc
>> MotionCorr/job008/Micrographs/*.mrc
>>
>> This would appear to tally with the recent discussion.
>>
>> However, upon moving to CTF Estimation using CTFFind4.1.5 within
>> the GUI (and requesting that micrographs without dose-weighting
>> are used for this), the consequent micrographs_ctf.star file
>> arrangement is:
>>
>> _rlnMicrographNameNoDW #1
>> _rlnMicrographName #2
>> _rlnCtfImage #3
>> [unnecessary lines omitted]
>> MotionCorr/job008/Micrographs/*.mrc
>> MotionCorr/job008/Micrographs/*_noDW.mrc
>> CtfFind/job009/Micrographs/*.ctf:mrc
>>
>> It would appear that Relion has somehow swapped the dose-weighted
>> and non-dose-weighted filenames in the .star file, resulting in
>> downstream processing that appears to use the non-dose-weighted
>> data (e.g. particles are extracted from _noDW.mrc files).
>>
>> Can I confirm that this is the case, and if so, whether there a
>> simple workaround? I guess one could rename the .star file flags,
>> though I'm not sure whether the order of these is important for
>> Relion.....?
>>
>> Alternatively, please advise if I have completely misunderstood
>> something!
>>
>> With kindest regards,
>>
>> Neil
>>
>>
>>
>>
>> On 13/12/2017 12:20, Sjors Scheres wrote:
>>
>> Hi again,
>>
>> So, the issue below is not an issue: it is as expected. After
>> running the wrapper around motioncor2 in RELION, the names of
>> the files SHOULD BE:
>> _noDW.mrc for the non-dose-weighted average
>> .mrc for the dose-weighted average.
>>
>> HTH,
>> Sjors
>>
>> PS: My apologies for the reply a while ago, where I had it the
>> other way around.
>>
>>
>> On 12/12/2017 08:25 PM, Niks J wrote:
>>
>> Hi Ambrose
>>
>> I am having similar issue with relion2. I have both
>> noDW.mrc and .mrc
>> files
>> Did you get it resolved? Did you have to rename the file
>> manually?
>>
>> Thanks,
>> Nikhil
>>
>>
>> Nikhil Jain, PhD
>> Postdoctoral Research Associate
>> Laboratory of Prof. Robert A. Britton
>> Department of Molecular Virology & Microbiology
>> Alkek Center for Metagenomics and Microbiome Research
>> Baylor College of Medicine
>> One Baylor Plaza, Room 607T
>> Houston, TX (USA) 77030
>>
>>
>>
>> On Thu, Nov 30, 2017 at 9:53 AM, Ambrose Plante
>> <[log in to unmask] <mailto:[log in to unmask]>>
>> wrote:
>>
>> Hi Sjors,
>>
>>
>> Thank you for your response. I indeed have both the
>> .mrc and the noDW.mrc
>> files and they seem to have been processed correctly,
>> so I can just
>> manually rename them to Relion's format if need be.
>>
>>
>> There are no errors or warnings in the logs, but I did
>> accidentally use an
>> older Motioncor2 executable. I will retry with the
>> latest release and see
>> if this fixes the issue.
>>
>>
>> Thank you,
>>
>>
>> Ambrose
>> ------------------------------
>> *From:* Sjors Scheres <[log in to unmask]
>> <mailto:[log in to unmask]>>
>> *Sent:* Thursday, November 30, 2017 6:20:18 AM
>> *To:* Ambrose Plante; [log in to unmask]
>> <mailto:[log in to unmask]>
>> *Subject:* Re: [ccpem] Relion-MotionCor2 naming issue
>>
>> Hi Ambroise,
>> Motioncor2 writes out .mrc and noDW.mrc, RELION will
>> rename this to
>> DW.mrc and .mrc respectively. Perhaps that last part
>> wasn't done for
>> some reason? Are there any errors/warnings? Did the
>> version of
>> MotionCor2 change perhaps?
>> Sjors
>> On 11/30/2017 03:36 AM, Ambrose Plante wrote:
>>
>> After employing motioncor2 through Relion,
>> including the dose-weighting
>>
>> flag, I have encountered a strange issue. Relion
>> outputs the suffix of the
>> dose-weighted average images as noDW.mrc, instead of
>> DW.mrc. I have not
>> encountered this error before and I have not seen
>> anyone talk about it on
>> the forums.
>>
>> Does this mean that dose-weighting has failed? Or
>> are the images fine
>>
>> and this is just a minor naming error?
>>
>> Running the motioncor2 outside of Relion fixes the
>> issue, but I would
>>
>> rather run it within Relion to keep the data structure
>> and workflow
>> consistent.
>>
>> Thank you,
>>
>> Ambrose Plante
>> Weill Cornell
>>
>> -- Sjors Scheres
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue, Cambridge Biomedical Campus
>> Cambridge CB2 0QH, U.K.
>> tel: +44 (0)1223 267061
>> <tel:%2B44%20%280%291223%20267061> <+44%201223%20267061>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www2
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www2>.
>> mrc-2Dlmb.cam.ac.uk_groups_scheres&d=DwICaQ&c=lb62iw4YL4RFalcE2hQUQealT9-
>>
>> RXrryqt9KZX2qu2s&r=grHw73qIGEHcQrES6UKBFXtBfxeZE2jlsA74Gk38jGY&m=
>> u5QtdOv0jWSwiNcxrD2oXPm2FLvVIIyHVWtI4-jiab4&s=fUf63sElb-
>> OUH9MGk0R2t2wAuz6qfYgVpLFa1cefamw&e=
>>
>>
>>
>>
>>
>> -- Dr. Neil Rzechorzek
>> Department of Biochemistry
>> University of Cambridge
>> Sanger Building
>> 80 Tennis Court Road
>> Cambridge, UK
>> CB2 1GA
>>
>> www.bioc.cam.ac.uk <http://www.bioc.cam.ac.uk>
>>
>> Advisory Chairman - Entrepreneurial Postdocs Of Cambridge
>>
>> www.epoc.group.cam.ac.uk <http://www.epoc.group.cam.ac.uk>
>>
>> Email: [log in to unmask] <mailto:[log in to unmask]>
>> Tel: +44 (0)1223 333652 <tel:%2B44%20%280%291223%20333652>
>>
>>
>>
>>
>> --
>> Nikhil Jain
>
>
--
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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