Appion

The origin is caused by origin not set correctly in the mrc file. However, it didn't bother older Chimera used in production at NRAMM. I now get this problem with Chimera 1.5.3

Neil, Do you know the Chimera command or python equivalent of "Center" in volume viewer dialog that I can add to apChimSnapShot.py or any recollection about this kind of problem/solution in the past?

The following are the specifics for reference.

I am running appion on CentOS 6 test computer with a model from our database. The mrc file header xyz origin are all at, strangely, -4.156. -41.5 grid step would have been more meaningful since the volume is 84x84x84.

The script used is:

uploadModel.py   --file=/home/acheng/GroEL_model.mrc --runname=file_12jan16p57   --session=sample --apix=3.3 --res=30 --symmetry=25 --contour=1.5   --mass=750 --zoom=1.0 --description='NRAMM ap234 ID3 import'   --rundir=/myamiImages/appion/sample/models/accepted/file_12jan16p57   --projectid=1 --expId=4 --jobtype=uploadmodel

upload-GroEL_model_12jan16u20u20_mrc.py generated by this scrip and apChimSnapShot.py has

viewerInfo = {'cameraAttrs': {'center': (0, 0, 0),...

while if I save the session with centered volume viewer dialog, it becomes

viewerInfo = {'cameraAttrs': {'center': (132.115, 136.368, 134.759),...