Thank you Mario! That is very helpful.
best,
Sjors
> Hi Sjors,
> Thank you for the excellent tutorial. I found a minor error in the
> tutorial. When trying to run "relion_prepare_subtomograms.py" as
> published in the WIKI, there was an error and it did not run. I traced
> the problem back to the file names in all_tomograms.star:
> data_
> loop_
> _rlnMicrographName
> ./Tomograms/05/IS002_291013_005.mrc
> ./Tomograms/06/IS002_291013_006.mrc
> ./Tomograms/07/IS002_291013_007.mrc
> ./Tomograms/08/IS002_291013_008.mrc
> ./Tomograms/09/IS002_291013_009.mrc
> ./Tomograms/10/IS002_291013_010.mrc
> ./Tomograms/11/IS002_291013_011.mrc
>
> This file was generated by issuing the following commands as indicated
> by the tutorial:
> relion_star_loopheader rlnMicrographName > all_tomograms.star
> ls ./Tomograms/*/*.mrc >> all_tomograms.star
>
> Using these commands the characters "./" were introduced at the
> beginning of each line. This confuses the Python script that parses the
> name by separating the root from the extension using "split('.')
>
> # Parsing the micrograph names
> micsplit = mic.split('.')
> microot = micsplit[0]
> dirsplit = microot.split('/')
>
> The tutorial needs to be corrected to read:
>
> ls Tomograms/*/*.mrc >> all_tomograms.star
>
>
>
>
> On 11/19/2015 08:50 AM, Sjors Scheres wrote:
>> Dear RELION users,
>>
>> We have recently submitted a manuscript about sub-tomogram averaging
>> in RELION to Nature Protocols, where it is currently under review.
>> Meanwhile, we also put a preprint of this paper at bioRxiv
>> (http://biorxiv.org/content/early/2015/11/03/030544), so you can
>> already read it.
>>
>> This paper is accompanied by an EMDB/EMPIAR entry
>> (https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10045/) that was
>> released today. This entry contains the input data as well as the
>> intermediate and final results that we obtained using the procedure
>> described in the manuscript. We hope that together they form an
>> efficient way to learn sub-tomogram averaging in RELION.
>>
>> Have fun,
>> Sjors
>>
>>
>>
>
> --
> +---------------------------------+
> | Mario J. Borgnia, Ph. D. |
> | |
> | Lab of Cell Biology |
> | NIH NCI/CCR |
> | 50 South Drive Rm 4306 MSC 8008 |
> | Bethesda MD 20892-8008 |
> | |
> | Tel: (301) 594 0563 |
> | [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
|