| # | Script Name | |
| 1 | align | #all script for align in spider |
| 2 | batchboxer.csh | #EMAN1 change box size |
| 3 | copy2smb.sh | #copy to smb server |
| 4 | ctf_filter2rl.sh | #filter micrographs by defocus/resolution from ctffind4 and generate .star file for Relion |
| 5 | DfCorrY.sh | #script to run Agard motincorr 1.0 |
| 6 | Dflog_list.sh | #chack micrographs for missing frame [black] |
| 7 | dm2mrcMoCoFFT.sh | #script to run old motioncorr |
| 8 | sxctf_filter2rl.sh | #filter micrographs by defocus/resolution form sxctre.py and generate .star file for Relion |
| 9 | dm3tomrc_s | #convert .dm3 to .mrc |
| 10 | dm4tomrc.sh | #convert .dm4 to .mrc |
| 11 | Frop_dm4Stk.sc | #Teru script for motincorr 1.0 |
| 12 | list_ctffind4_V3.sh | #make list of ctf parameters from ctffind4 |
| 13 | loop4dm.sh | #convert .dm4 to .mrc and copy to new dir |
| 14 | motioncorr2_1.sh | #script to run motioncorr 2.1 |
| 15 | mrc_rescale.sc | #script to rescale the mrc file, and reverse the contrast |
| 16 | RCToutput.sh | #write output from RCT e2boxer |
| 17 | toBinned.sh | #bined file |
| 18 | toHdf.sh | #convert .dm3 to .hdf |
| 19 | toRenameInc.sh | #change file name&number |
| 20 | stack2spier | #make stack for spider |
| 21 | gctf.sh | #ctf parameter on GPU using Gctf (can be use for CTF for tilt) |
| 22 | gpick | #autopick on GPU using Gautomatch |
| 23 | sxcter.py | #script to run sxcter on Accre |
| 24 | sb2accre_template.sh | #template slurme script to run software from SBgrid on ACCRE |
| 25 | mpc_rt.com | #script to do on-the-fly data processing (dm4 motioncorr Gautomatch Gctf) |