upload helical picking from EMAN1/2 to Appion
Added by Rui Zhang over 6 years ago
Dear Appion developers,
Is it possible to upload helical pick coordinates from EMAN helixboxer program to Appion?
The EMAN helical pick coordinates file contains start and end points, like this:
1439 125 400 400 -1
2549 1284 400 400 -2
1632 2431 400 400 -1
837 1637 400 400 -2
858 2571 400 400 -1
2320 1309 400 400 -2
18 3410 400 400 -1
854 2571 400 400 -2
I tried to convert it and upload it as Appion particle list file, but it didn't work.
By "working" I mean when one tries to use the helical picking to do "Stack Creation", the "Helical Step (in Ångstroms)" option will show up on the right side.
My format of the Appion particle list is like this:
particle# x_coord y_coord helix_num image_name
1 824 48 1 17dec14a_imagename1
2 2012 1208 1 17dec14a_imagename1
3 2916 1968 1 17dec14a_imagename1
4 3780 2536 1 17dec14a_imagename1
5 64 148 2 17dec14a_imagename1
6 1500 2144 2 17dec14a_imagename1
Thank you!
Rui Zhang
......
Replies (3)
RE: upload helical picking from EMAN1/2 to Appion - Added by Anchi Cheng over 6 years ago
I created Issue #5389.
Please upload an actual list file and the full command used in upload there. You may substitute local-specific information in the commad you post, but please keep the list file format unchanged. It is likely a problem with the format of the file.
RE: upload helical picking from EMAN1/2 to Appion - Added by Rui Zhang over 6 years ago
Hi, Anchi,
Thanks for the quick reply!
Please see my helixboxer file and appion particle list file in the attachment.
I wrote a script to convert a bunch of helixboxer files into one appion particle list file.
The command I use to upload the file is:
/home/ruiz/myami-3.2/appion/bin/uploadAppionParticles.py \
--filename=/data2/MTs/helixboxer/particledata-test.dat --session=17dec01x \
--diam=250 --commit --rundir=/data/appion/ruiz/17dec01x/extract/manual1 \
--runname=manual1 --projectid=9 --expid=45 --jobtype=uploadparticles
RE: upload helical picking from EMAN1/2 to Appion - Added by Rui Zhang over 6 years ago
BTW, this is the script I used to convert a bunch of helixboxer files into one appion particle list file.
| convert.py (541 Bytes) convert.py |