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Extra instructions for commands

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Michael A. Cianfrocco edited this page Mar 3, 2017 · 12 revisions

Under development

Micrographs must be placed within directory called 'Micrographs'

For movie alignment:

  • Adding '--binnedMicsOnly' into the extra command space of the Relion GUI will only download binned by 4 micrographs to your local machine, saving the full micrographs on the cloud
  • Including s3-{bucketname} into Input movies STAR file will have script start with movies already on the cloud
  • If s3-{bucketname} ; take name and folder name from aws_listprojects output. Script will add s3://{teamname}-{keyname}: s3-empiar-10061/motioncorr-job007/
  • Will look for path to gain ref locally or on s3 (and will skip gain ref in bucket if it comes across it)

For CTF estimation:

  • Including s3-{bucketname} into Input movies STAR file will have script start with movies already on the cloud
  • Only supporting Gctf at this time

For movie refinement - this will assume that the Import/micrographs.star file ALREADY has a corresponding S3 bucket in the cloud. this script will not be able to upload all movies at this point.

In general - remove any weird symbols from Relion GUI - sometimes they show up for software paths.

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