Feature #3922
closedFrealign 9 with Appion
0%
Description
Dear Anchi,
The Frealign app in Appion is quite good and goes almost all the way to getting the Frealign run ready, except for a few bits. Directory of the run is here: /gpfs/appion/yztan/15sep14b/recon/frealign_recon5/
1) Converting the parameter file in the directory for Frealign9 format using
python -c 'from appionlib import apFrealign ; apFrealign.frealign8_to_frealign9("params.000.par", "output.par", apix of the stack used for Xmipp refinement, occ=100)'
2) Running Frealign9
The Frealign8 refinement did not run, probably because it was not installed as a module in the SEMC cluster
Thank you!
Updated by Anchi Cheng over 8 years ago
- Assignee changed from Anchi Cheng to Yong Zi Tan
Yong Zi,
What is a good version of Frealign I should use for development ?
Updated by Yong Zi Tan over 8 years ago
I would suggest using V9.11, the latest stable version.
Updated by Anchi Cheng over 8 years ago
Can you point me to a frealign run you have outside appion ? I need to examine the mparameters and the shell scripts it generates.
Updated by Anchi Cheng over 8 years ago
- Status changed from New to Assigned
- Assignee changed from Yong Zi Tan to Anchi Cheng
- Target version set to Appion/Leginon 3.3
r19499 convert the old-style single refinement frealign implementation to V9.11 Tested as setup script
To Do:
1. test on cluster
2. test upload
3. convert to use mparameters and frealign_run_refine as done in frealign documentation.
Note: I will not merge this to 3.2
Updated by Anchi Cheng over 6 years ago
- Status changed from Assigned to Won't Fix or Won't Do
Preparation certainly works. The rest is unlikely be used any more even though it probably works now that there is cisTEM.