diff --git a/config/templates/scipion.template b/config/templates/scipion.template index 68cfd88765..cc81980b0c 100644 --- a/config/templates/scipion.template +++ b/config/templates/scipion.template @@ -21,7 +21,7 @@ EM_ROOT = software/em BSOFT_HOME = %(EM_ROOT)s/bsoft-1.9.0 CTFFIND_HOME = %(EM_ROOT)s/ctffind-3.6 -CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.5 +CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.8 DOGPICKER_HOME = %(EM_ROOT)s/dogpicker-0.2.1 EMAN2DIR = %(EM_ROOT)s/eman-2.12 ETHAN_HOME = %(EM_ROOT)s/ethan-1.2 diff --git a/install/script.py b/install/script.py index bdbc2f1fa3..1b65126772 100644 --- a/install/script.py +++ b/install/script.py @@ -387,6 +387,9 @@ env.addPackage('ctffind4', version='4.1.5', tar='ctffind_V4.1.5.tgz') +env.addPackage('ctffind4', version='4.1.8', + tar='ctffind_V4.1.8.tgz') + env.addPackage('summovie', version='1.0.2', tar='summovie_1.0.2.tgz') diff --git a/pyworkflow/em/packages/grigoriefflab/grigoriefflab.py b/pyworkflow/em/packages/grigoriefflab/grigoriefflab.py index 168404c87b..3bd146baf6 100644 --- a/pyworkflow/em/packages/grigoriefflab/grigoriefflab.py +++ b/pyworkflow/em/packages/grigoriefflab/grigoriefflab.py @@ -53,7 +53,7 @@ def getSupportedVersions(var='FREALIGN'): if var == 'UNBLUR': return ['1.0_150529', '1.0.2'] elif var == 'CTFFIND4': - return ['4.0.15', '4.1.5'] + return ['4.0.15', '4.1.5', '4.1.8'] else: # FREALIGN return ['9.07'] diff --git a/pyworkflow/em/packages/grigoriefflab/protocol_ctffind.py b/pyworkflow/em/packages/grigoriefflab/protocol_ctffind.py index fbf5c58b9f..f7ac54d357 100644 --- a/pyworkflow/em/packages/grigoriefflab/protocol_ctffind.py +++ b/pyworkflow/em/packages/grigoriefflab/protocol_ctffind.py @@ -256,7 +256,7 @@ def _prepareCommand(self): self._params['stepPhaseShift'] = self.stepPhaseShift.get() else: self._params['phaseShift'] = "no" - if self.resamplePix: # ctffind v4.1.5 + if self.resamplePix: # ctffind >= v4.1.5 self._params['resamplePix'] = "yes" else: self._params['resamplePix'] = "no" @@ -294,7 +294,7 @@ def _prepareRecalCommand(self, ctfModel): self._params['stepPhaseShift'] = self.stepPhaseShift.get() else: self._params['phaseShift'] = "no" - if self.resamplePix: # ctffind v4.1.5 + if self.resamplePix: # ctffind >= v4.1.5 self._params['resamplePix'] = "yes" else: self._params['resamplePix'] = "no" @@ -335,7 +335,7 @@ def _argsCtffind4(self): %(maxDefocus)f %(step_focus)f""" - if getVersion('CTFFIND4') == '4.1.5': + if getVersion('CTFFIND4') in ['4.1.5', '4.1.8']: if self.findPhaseShift: self._args += """ no @@ -402,7 +402,7 @@ def _getCTFModel(self, defocusU, defocusV, defocusAngle, psdFile): def _summary(self): summary = em.ProtCTFMicrographs._summary(self) - if self.useCtffind4: + if self.useCtffind4 and getVersion('CTFFIND4') == '4.1.5': summary.append("NOTE: ctffind4.1.5 finishes correctly (all output is generated properly)," " but returns an error code. Disregard error messages until this is fixed." "http://grigoriefflab.janelia.org/node/5421")