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 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.	dosefgpu_driftcorr			#Yifan motion correction software v2.1
12.	Frop_dm4Stk.sc				#Teru script for motincorr 1.0
13.	Gautomatch-v0.50_sm_30_cu5.5_x86_64	#Gautomatch software
14.	Gctf-v0.50_sm_30_cu5.5_x86_64		#Gctf software
15.	list_ctffind4_V3.sh			#make list of ctf parameters from ctffind4
16.	loop4dm.sh				#convert .dm4 to .mrc and copy to new dir
17.	motioncorr				#Yifan motion correction software v
18.	motioncorr2_1.sh			#script to run motioncorr 2.1
19.	mrc_rescale.sc				#script to rescale the mrc file, and reverse the contrast
20.	RCToutput.sh				#write output from RCT e2boxer
21.	toBinned.sh				#bined file
22.	toHdf.sh				#convert .dm3 to .hdf
23.	toRenameInc.sh				#change file name&number
24.	UcsfDfCorr-12-27-2015			#Agard motion correction software
25.	stack2spier				#make stack for spider
26.	gctf.sh					#ctf parameter on GPU using Gctf can do CTF for tilt
27.	gpick					#autopick on GPU using Gautomatch
28.	sxcter.py				#script to run sxcter on Accre
29.	sb2accre_template.sh			#template slurme script to run software from SBgrid on ACCRE
30.	mpc_rt.com				#script to do on-the-fly data processing (dm4 motioncorr Gautomatch Gctf)