Appion

currently only works from command line.

example command¶

polishStack.py -h

polishStack.py --stack-id=283 --projectid=7 --rundir=/data2/log-l/appion/15jul16a/stacks/polish1 --runname=polish1 --ddstackid=33 --micrographs_per_job=2 --expid=14140 --particleradius=125 --expweight --localavg

Some details on running¶

• requires an unaligned, but gain-normalized ddframestack (provided by --ddstackid option)
• currently will create an unbinned stack only
• queries database for all relevant parameters, including microscope kv, image dose, number of frames, etc
• requires install of alignparts_lmbfgs.exe from John Rubinstein. Can be located in myami/appion/bin directory
• many options are available (e.g. contrast inversion)

stitch MRC stack¶

To create an identical stack as your input, in MRC format, run polishStackStitch.py with same general options as above, for example:

polishStackStitch.py --stackid=283 --projectid=7 --rundir=/data2/log-l/appion/15jul16a/stacks/polish1 --runname=polish1 --ddstackid=33 --expid=14140

known issues¶

• launches a bunch of small jobs. If your scheduler is not set up to launch jobs from slave nodes, then you need to run script from command line on head node. This could use improvements in implementation in code.

Future improvements can include¶

• web gui in stack category
• stack uploader