Hi Valerie,
--continue is a valid option. Page 7 of the tutorial might help. I would
really recommend using the GUI if you are not already.
HTH,
Sjors
On 02/14/2018 04:00 PM, Valerie Biou wrote:
> dear Relion users,
>
> I am new to cryo-EM and Relion and I am lucky enough to have access to a bioinformatics cluster with GPUs to perform calculations. It has a 24h wall time that might be doubled if really needed, but other people are running MD simulations and also need to access the machine.
>
> Calculations up to auto_refine worked ok. However, 3D auto_refine returned no result after 24 hours, so I have no idea how many cycles it performed.
> The option "relion_refine —continue" seems to allow programming the number of cycles and restart afterwards. however, it is not listed in the standard "relion_refine —help" result and it returns options that are marked OLD. Is it really obsolete or could we use it with re-entry after a few cycles? if yes, which options should we use?
>
> In summary, I would like to know how people run their 3D refinements.
> Do people use GPU clusters with longer time walls, or individual machines ?
>
> thanks for sharing your experience.
> all the best,
>
> Valérie
--
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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