*************************************************************************************** Relion workflow data preprocessing: ======================================================================================= 1. transfer dm4 file from Polara ex-raid\Cryo-GPU to your working computer [use ssh app on the K2 computer] 2. If needed rename/renumber the dm4 file [toRenameInc.sh] 3. back-up the dm4 file. finish this step befor mooving to motion correction or modify the script !!!! 4. motion correction .dm4 --> .mrcs --> .mrc [DfCorrY.sh/dm2mrcMoCoFFT.sh/motioncorr2_1.sh/] 5. check for black frame [Dflog_list.sh] 6. delete .mrcs file 7. copy mrc file to working Dir in DORS 8. for RELION make .star file 9. CTF4 [ctffind4.slurm] or other CTF app [sxcter.py/gctf.sh] 10 get the ctf4 parameters [list_ctffind4_V3.sh] 11. filter your micrographs ctf parameter list and get ride from bad micrographs (resolution, defocus astigmatisem)[ctf_filter2rl.sh/sxctf_filter2rl.sh] 12. pick manualy or autopick can be done in relion, eman2, Gautometch. [autopick.slurm/gpick.sh] 13. extract the partical. if you done autopick you can sort the particles (get z-score and filter bad particles) 14. 2D class in relion [2Dclass.slurm] or eman2 (you can transfer your relion project to eman2 with e2reliontoeman.py script, use --help or from the eman gui) 15. 3D class in relion [3Dclass.slurm] *************************************************************************************** Modification if using real-time proccesing ======================================================================================= *** if you use real-time you all-ready done at list dm4-->mrc, motion correction and ctf. 1. to use real-time proccesing use [Motioncorr_Gautomatch_Gctf_Real-time_Auto-run_dm4.com] script 2. transfer the sum.mrc and movie.mrcs file to your dors Dir and backup the .dm4 file 3. delete everything from cryo-GPU for next user 4. for RELION make .star file 5. get the ctf4 parameters [list_ctffind4_V3.sh] 6. filter your micrographs ctf parameter list and get ride from bad micrographs (resolution, defocus astigmatisem)[ctf_filter2rl.sh/sxctf_filter2rl.sh] 7. pick manualy or autopick can be done in relion, eman2, Gautometch. [autopick.slurm/gpick.sh] 8. extract the partical. if you done autopick you can sort the particles (get z-score and filter bad particles). whet you extract it will be smart to downsample the particles by 2-4 to get this faster. 9. 2D and 3D class when you have good class extract agian with thh origenl samole size and go to autorefine. *************************************************************************************** ACCRE ======================================================================================= 1. log in with==> ssh -Y userID@login.accre.vanderbilt.edu 2. type PW 3. workin Dir. 1- dors ==> /dore/lab-name/home/usderID/accre 2- home or scretch (limited vol not backup) 4. transfer data to home ==> scp my_file userID@vmplogin.accre.vanderbilt.edu:~/dir [add -c blowfish for faster copy] 5. for autopick put more then 5GB mem 6. 2D 100 calss with 50k particle take more then 7h 7. to get information on job: sacct --format JobID,jobname,NTasks,nodelist,MaxRSS,MaxVMSize,AveRSS,AveVMSize or sstat 8. information on job: scontrol Show job 9. information on job: rtractjob 10. 11. 12. 13. 14. 15.