Feature #4489
Updated by Anchi Cheng about 8 years ago
GCTF fails right now because it can't find the 'extra_phase_shift' parameter. Also, the newest version released September 29 supports phase plate parameters, these should be added to the Appion GUI. 'defocus2': 2.2458909999999999e-06, 'defocusinit': 1.9999999999999999e-06, 'do_EPA': '1', 'graph1': '/gpfs/appion/cnegro/16sep30g/gctf/gctfrun4/opimages/16sep30g_04gr_02sq_02hln_02enn-a-pow.jpg', 'imagenum': 1, 'volts': 300000} {aceparams: None, ctftilt_params: None, xmipp_ctf_params: None, ace2_params: None, ctffind4_params: DataReference[class: ApCtfFind4ParamsData, dmid: (('node43', 49152), 237), dbid: 12, referent: weak], session: DataReference[class: SessionData, dmid: (('node43', 49152), 240), dbid: 2691, referent: weak], path: DataReference[class: ApPathData, dmid: (('node43', 49152), 241), dbid: 1732, referent: weak], name: gctfrun4, hidden: False} '/gpfs/appion/cnegro/16sep30g/gctf/gctfrun4' ... Committing ctf parameters for 16sep30g_04gr_02sq_02hln_02enn-a to database Traceback (most recent call last): File "/opt/myamisnap/bin/gctf.py", line 457, in <module> imgLoop.run() File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 95, in run self.loopCommitToDatabase(imgdata) File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 153, in loopCommitToDatabase return self.commitToDatabase(imgdata) File "/opt/myamisnap/bin/gctf.py", line 408, in commitToDatabase ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir']) File "/opt/myamisnap/lib/appionlib/apCtf/ctfinsert.py", line 43, in validateAndInsertCTFData ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq) File "/opt/myamisnap/lib/appionlib/apCtf/ctfinsert.py", line 83, in runCTFdisplayTools ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq) File "/opt/myamisnap/lib/appionlib/apCtf/ctfdisplay.py", line 1131, in makeCtfImages ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod) File "/opt/myamisnap/lib/appionlib/apCtf/ctfdisplay.py", line 969, in CTFpowerspec self.extra_phase_shift = to_float(ctfdata['extra_phase_shift']) KeyError: 'extra_phase_shift' [cnegro@node43 ~]$