• EMEN2
• EMAN2_Integration

EMEN2 - EMAN2 Integration

In addition to batch upload/download support, emen2client.py offers some basic EMAN2 synchronization capabilities. These are still being developed, but are already useful.

[irees@mbp ~/data]$ emen2client.py sync --help

Usage: emen2client.py sync [options] <project record ID>
                
This program will upload CTF parameters, boxes, and particle sets into an EMEN2 database. Because filenames are not always globally unique, you must specify a base project that will be searched for files.

If run with "--check", it will only test to see if it can make the correct file mappings between the local EMAN2 project and the remote database. Nothing will be written. This is a good way to test to see if the correct mappings can be made before you attempt to commit any changes.
                
Options:
  -h, --help            show this help message and exit
  -U USERNAME, --username=USERNAME
                        Username
  -P PASSWORD, --password=PASSWORD
                        Password (Note: specifying passwords in shell commands
                        is not secure)
  -H HOST, --host=HOST  Host endpoint URI
  -C CTXID, --ctxid=CTXID
                        Valid Context ID
  --check               Do not upload anything; just check file mappings
  --ctf                 Upload CTF Parameters
  --boxes               Upload Boxes
  --eman1               Look in EMAN1-style files instead of EMAN2 project
                        database
  --ptcls               Upload Particle Sets

Upload CTF parameters

The "--ctf" option will search for CTF parameters in several places.

If EMAN1 files are being searched (--eman1), ctfparm.txt in the local directory will be checked. Otherwise, two locations are checked for EMAN2 CTF parameters. First, any phase flipped particles that have been written out will be checked, as these are considered more authoritative than the e2ctf.py settings. If particles have been corrected but not written out, the script will then use the values from the e2ctf.py settings.

Upload box coordinates

The "--boxes" option will search for particle coordinates to upload to the database. They will be attached to the CCD or Scan record as a "box" child. The coordinates are attached as a .box file, in EMAN1 format.

EMAN1 boxes are loaded from .box files in the local directory. EMAN2 box locations are read from the "ptcl_source_coords" tag in the particle headers.

Upload particle stacks

This feature is still being implemented

Download

THis feautre is still being implemented