Hi Nikhil,

The wrapper around RELION will use a std::rename call to move the files 
around:
X.mrc -> X_noDW.mrc
X_DW.mrc -> X.mrc
This is because of internal naming conventions inside RELION.

If you get the
"ERROR in renaming: MotionCorr/job005/Micrographs_no_align_2/X_DW.mrc to 
MotionCorr/job005/Micrographs_no_align_2/X.mrc"
then, this renaming failed for some reason. I am not sure why, perhaps 
your sys admin has an idea about this?
In the case you get this error, the X_DW.mrc is the dose-weighted 
micrograph, which you probably want to use! You could manually rename 
the files before moving forward in RELION.

In general, ERROR messages in red in the error window of the GUI should 
probably not be ignored. How many other people get this error?

HTH,
Sjors


On 12/12/2017 10:44 PM, Niks J wrote:
> This adds to the confusion
> because The error I am getting is this :
>
> "ERROR in renaming: MotionCorr/job005/Micrographs_no_align_2/X_DW.mrc to
> MotionCorr/job005/Micrographs_no_align_2/X.mrc"
>
>
> As per this error relion could not convert X_DW.mrc file to .mrc and I
> still don't see X_DW.mrc in my directory. Instead I have X_noDW.mrc and
> X.mrc.
>
>
> The question is how is this X.mrc is being generated and whether  X.mrc is
> dose weighted or not.
>
>
> Sorry If I am making it more complicated.
>
> Best,
> Nikhil
>
> On Tue, Dec 12, 2017 at 4:09 PM, Shawn Zheng <[log in to unmask]> wrote:
>
>> Hi Ambrose,
>>
>> MotionCor2 always writes out .mrc file and optionally DW.mrc files when
>> the required input parameters (pixel size, frame dose, and voltage) are
>> provided in the command line to MotionCor2.
>>
>> .mrc file is NOT dose-weighted. DW.mrc is dose-weighted. MotionCor2 does
>> not generate noDW.mrc. It has been this way since MotionCor2 was first
>> released.
>>
>> Best
>> Shawn
>>
>> On Tue, Dec 12, 2017 at 1:29 PM, Ambrose Plante <[log in to unmask]>
>> wrote:
>>
>>> Hi Niks,
>>>
>>>
>>> I tried multiple combinations of MotionCor2 releases as well as the
>>> stable Relion and beta Relion. All of them came up with the same issue. I
>>> renamed the files manually and continued on the Relion pipeline.
>>>
>>>
>>> This indeed "worked", however:
>>>
>>>
>>> Interestingly, after re-extracting particles using a data.star from a
>>> previously refined structure on what I assumed to be the dose-weighted
>>> files from Sjors' answer (.mrc), the new particles refined to about half of
>>> an angstrom lower resolution than the originals. Also, particle polishing
>>> with the aligned movie frames from this motioncor2 run results in shiny
>>> particles which refine to a slightly worse structure. This makes me think
>>> that either I am doing something wrong during motion-correction or that
>>> something is compiled strangely on my cluster.
>>>
>>>
>>> I will let you know what I find.
>>>
>>>
>>> Ambrose
>>> ------------------------------
>>> *From:* Niks J <[log in to unmask]>
>>> *Sent:* Tuesday, December 12, 2017 3:25:11 PM
>>> *To:* Ambrose Plante
>>> *Cc:* [log in to unmask]
>>> *Subject:* Re: [ccpem] Relion-MotionCor2 naming issue
>>>
>>> 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]>
>>> 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]>
>>> *Sent:* Thursday, November 30, 2017 6:20:18 AM
>>> *To:* Ambrose Plante; [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 <+44%201223%20267061>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrc
>>> -2Dlmb.cam.ac.uk_groups_scheres&d=DwICaQ&c=lb62iw4YL4RFalcE2
>>> hQUQealT9-RXrryqt9KZX2qu2s&r=grHw73qIGEHcQrES6UKBFXtBfxeZE2j
>>> lsA74Gk38jGY&m=u5QtdOv0jWSwiNcxrD2oXPm2FLvVIIyHVWtI4-jiab4&s
>>> =fUf63sElb-OUH9MGk0R2t2wAuz6qfYgVpLFa1cefamw&e=
>>>
>>>
>>>
>>>
>>> --
>>> 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