From 00535a409575eb023893a5b047407d8fdd8b780b Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 13:36:28 +0100 Subject: [PATCH 01/16] Update XChemRefine.py Fixing issue with HKLIN and XYZIN --- xce/lib/XChemRefine.py | 146 ++++++++++++++++++----------------------- 1 file changed, 64 insertions(+), 82 deletions(-) diff --git a/xce/lib/XChemRefine.py b/xce/lib/XChemRefine.py index f206ec86..1e276e5c 100755 --- a/xce/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -873,7 +873,7 @@ def RunRefmac( os.path.join(self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz") ): RefmacParams["HKLIN"] = "HKLIN " + os.path.join( - self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz \\\n" + self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz" ) else: Logfile.error( @@ -884,19 +884,19 @@ def RunRefmac( self.ProjectPath, self.xtalID, "Refine_" + Serial, - "refine_" + Serial + ".mtz \\\n", + "refine_" + Serial + ".mtz", ) ####################################################### # XYZIN & XYZOUT RefmacParams["XYZIN"] = "XYZIN " + os.path.join( - self.ProjectPath, self.xtalID, "Refine_" + Serial, "in.pdb \\\n" + self.ProjectPath, self.xtalID, "Refine_" + Serial, "in.pdb" ) RefmacParams["XYZOUT"] = "XYZOUT " + os.path.join( self.ProjectPath, self.xtalID, "Refine_" + Serial, - "refine_" + Serial + ".pdb \\\n", + "refine_" + Serial + ".pdb", ) ####################################################### @@ -1069,101 +1069,83 @@ def RunRefmac( + '"\n' + "module load phenix/1.20\n" + "module load buster/20240123\n" - + "cd " - + self.ProjectPath - + "/" - + self.xtalID - + "/Refine_" - + Serial + + "module load ccp4\n" + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + Serial + "\n" - "\n" - + refinementStatus + + refinementStatus + "\n" + findTLS - + "refmac5 " - + RefmacParams["HKLIN"] - + RefmacParams["HKLOUT"] - + RefmacParams["XYZIN"] - + RefmacParams["XYZOUT"] - + RefmacParams["LIBIN"] - + RefmacParams["LIBOUT"] - + RefmacParams["TLSIN"] - + RefmacParams["TLSOUT"] - + " << EOF > refmac.log\n" - "make -\n" - " hydrogen ALL -\n" - " hout NO -\n" - " peptide NO -\n" - " cispeptide YES -\n" - " ssbridge YES -\n" - " symmetry YES -\n" - " sugar YES -\n" - " connectivity NO -\n" - " link NO\n" + RefmacParams["NCS"] + "refi -\n" - " type REST -\n" - " resi MLKF -\n" - " meth CGMAT -\n" + + "refmac5 " + + RefmacParams["HKLIN"] + " " + + RefmacParams["HKLOUT"] + " " + + RefmacParams["XYZIN"] + " " + + RefmacParams["XYZOUT"] + " " + + RefmacParams["LIBIN"] + " " + + RefmacParams["LIBOUT"] + " " + + RefmacParams["TLSIN"] + " " + + RefmacParams["TLSOUT"] + " " + + "<< EOF > refmac.log\n" + + "make -hydrogen ALL -hout NO -peptide NO -cispeptide YES -ssbridge YES -symmetry YES -sugar YES -connectivity NO -link NO\n" + + RefmacParams["NCS"] + + "refi -type REST -resi MLKF -meth CGMAT\n" + RefmacParams["BREF"] + RefmacParams["TLS"] + RefmacParams["TWIN"] + "ncyc " + RefmacParams["NCYCLES"] + + "scal -type SIMP -LSSC -ANISO -EXPE\n" + + weight + "solvent YES\n" + + "monitor MEDIUM -torsion 10.0 -distance 10.0 -angle 10.0 -plane 10.0 -chiral 10.0 -bfactor 10.0 -bsphere 10.0 -rbond 10.0 -ncsr 10.0\n" + + "labin FP=F SIGFP=SIGF FREE=FreeR_flag\n" + + "labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n" + + RefmacParams["TLSADD"] + "\n" - "scal -\n" - " type SIMP -\n" - " LSSC -\n" - " ANISO -\n" - " EXPE\n" + weight + "solvent YES\n" - "monitor MEDIUM -\n" - " torsion 10.0 -\n" - " distance 10.0 -\n" - " angle 10.0 -\n" - " plane 10.0 -\n" - " chiral 10.0 -\n" - " bfactor 10.0 -\n" - " bsphere 10.0 -\n" - " rbond 10.0 -\n" - " ncsr 10.0\n" - "labin FP=F SIGFP=SIGF FREE=FreeR_flag\n" - "labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT" - " FOM=FOM\n" + RefmacParams["TLSADD"] + "\n" - "DNAME " + self.xtalID + "\n" - "END\n" - "EOF\n" - "\n" - "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + + "DNAME " + self.xtalID + + "\n" + + "END\n" + + "EOF\n" + + "\n" + + "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + "/bin/mv molprobity.out refine_molprobity.log\n" - "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG" - " > validate_ligands.txt\n" % (Serial, Serial) - + "cd " - + self.ProjectPath - + "/" - + self.xtalID + + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n" % (Serial, Serial) + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + "\n" - "#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n" - % (self.ProjectPath, self.xtalID, Serial, Serial) - + "#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n" - % (self.ProjectPath, self.xtalID, Serial, Serial) + "ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n" % (Serial, Serial) + "ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n" % (Serial, Serial) + "ln -s refine.pdb refine.split.bound-state.pdb\n" - "\n" - "ln -s Refine_%s/validate_ligands.txt .\n" % Serial + + "\n" + + "ln -s Refine_%s/validate_ligands.txt .\n" % Serial + "ln -s Refine_%s/refine_molprobity.log .\n" % Serial + "mmtbx.validation_summary refine.pdb > validation_summary.txt\n" - "\n" - "fft hklin refine.mtz mapout 2fofc.map << EOF\n" - "labin F1=FWT PHI=PHWT\n" - "EOF\n" - "\n" - "fft hklin refine.mtz mapout fofc.map << EOF\n" - "labin F1=DELFWT PHI=PHDELWT\n" - "EOF\n" - "\n" + updateDB + "\n" - "/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n" % (self.ProjectPath, self.xtalID) + "\n" - "cd " + self.ProjectPath + "/" + self.xtalID + "/Refine_" + Serial + "\n" - "\n" + spider_plot + "\n" + + "fft hklin refine.mtz mapout 2fofc.map << EOF\n" + + "labin F1=FWT PHI=PHWT\n" + + "EOF\n" + + "\n" + + "fft hklin refine.mtz mapout fofc.map << EOF\n" + + "labin F1=DELFWT PHI=PHDELWT\n" + + "EOF\n" + + "\n" + + updateDB + + "\n" + + "/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n" % (self.ProjectPath, self.xtalID) + + "\n" + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + Serial + + "\n" + + spider_plot + + "\n" ) if os.path.isfile(xce_logfile): From c40f6092f18f4bc6efc66c4e3ac8f6eb3a91b8df Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 13:38:01 +0100 Subject: [PATCH 02/16] Update setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index fd08bd2e..29826470 100755 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name="xce", - version="1.5.0", + version="2.0.1", description="GUI tool for XChem", author="Tobias Krojer", packages=find_packages(), From 9988e07fc385ec2be05506bba0cbea509e4abe24 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 13:42:58 +0100 Subject: [PATCH 03/16] Update settings_preferences.py --- xce/gui_scripts/settings_preferences.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index db7843fe..ecbd80ea 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -23,7 +23,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = "v1.9.4" + xce_object.xce_version = "v2.0.1" # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -724,7 +724,11 @@ def dropdown_items(self, xce_object): ] xce_object.panddas_file_tasks = [ + "pre-run for ground state model", + "Build ground state model", + "------------------------------------------", "pandda.analyse", + "pandda.analyse (PanDDA2)", "pandda.inspect", "run pandda.inspect at home", "------------------------------------------", @@ -732,22 +736,18 @@ def dropdown_items(self, xce_object): "Export ALL PANDDA models", "Export SELECTED PANDDA models", "------------------------------------------", - "Show HTML summary", - "cluster datasets", - "Event Map -> SF", - "apo -> mmcif", - "check modelled ligands", - "------------------------------------------", "refine ALL bound-state models with BUSTER", "refine NEW bound-state models with BUSTER", "------------------------------------------", "refine ALL bound-state models with BUSTER (no sanity check)", "refine NEW bound-state models with BUSTER (no sanity check)", "------------------------------------------", - "pre-run for ground state model", - "Build ground state model", + "Show HTML summary", + "cluster datasets", + "Event Map -> SF", + "apo -> mmcif", + "check modelled ligands", "------------------------------------------", - "pandda.analyse (PanDDA2)", ] xce_object.refine_file_tasks = [ From debf9b2880f5d85ee5f7b0d77b1826a9dfb5069c Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 13:44:13 +0100 Subject: [PATCH 04/16] Update XChemLog.py --- xce/lib/XChemLog.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/xce/lib/XChemLog.py b/xce/lib/XChemLog.py index db1e518c..5740c30a 100755 --- a/xce/lib/XChemLog.py +++ b/xce/lib/XChemLog.py @@ -19,10 +19,7 @@ def create_logfile(self, version): " # #\n" " # Version: %s #\n" " # #\n" - " # Date: 10/10/2022 #\n" - " # #\n" - " # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n" - " # tobias.krojer@maxiv.lu.se #\n" + " # Date: 01/08/2024 #\n" " # #\n" " ###################################################################\n" "\n" % pasteVersion From 517717b1758420066b1a37c65ffdf1b061844811 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 13:48:45 +0100 Subject: [PATCH 05/16] Update XChemLog.py --- xce/lib/XChemLog.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/xce/lib/XChemLog.py b/xce/lib/XChemLog.py index 5740c30a..9428699f 100755 --- a/xce/lib/XChemLog.py +++ b/xce/lib/XChemLog.py @@ -19,7 +19,7 @@ def create_logfile(self, version): " # #\n" " # Version: %s #\n" " # #\n" - " # Date: 01/08/2024 #\n" + " # Date: 01/08/2024 #\n" " # #\n" " ###################################################################\n" "\n" % pasteVersion From 30362410c2f7f43a6c2384d4a82b958916d33ae5 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 13:49:57 +0100 Subject: [PATCH 06/16] Update settings_preferences.py --- xce/gui_scripts/settings_preferences.py | 1 - 1 file changed, 1 deletion(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index ecbd80ea..cdac5529 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -747,7 +747,6 @@ def dropdown_items(self, xce_object): "Event Map -> SF", "apo -> mmcif", "check modelled ligands", - "------------------------------------------", ] xce_object.refine_file_tasks = [ From ae09863ee989030597245d1182a2b7031b265ebf Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 13:58:12 +0100 Subject: [PATCH 07/16] Update settings_preferences.py --- xce/gui_scripts/settings_preferences.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index cdac5529..13e484a8 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -724,11 +724,7 @@ def dropdown_items(self, xce_object): ] xce_object.panddas_file_tasks = [ - "pre-run for ground state model", - "Build ground state model", - "------------------------------------------", "pandda.analyse", - "pandda.analyse (PanDDA2)", "pandda.inspect", "run pandda.inspect at home", "------------------------------------------", @@ -736,17 +732,22 @@ def dropdown_items(self, xce_object): "Export ALL PANDDA models", "Export SELECTED PANDDA models", "------------------------------------------", + "Show HTML summary", + "cluster datasets", + "Event Map -> SF", + "apo -> mmcif", + "check modelled ligands", + "------------------------------------------", "refine ALL bound-state models with BUSTER", "refine NEW bound-state models with BUSTER", "------------------------------------------", "refine ALL bound-state models with BUSTER (no sanity check)", "refine NEW bound-state models with BUSTER (no sanity check)", "------------------------------------------", - "Show HTML summary", - "cluster datasets", - "Event Map -> SF", - "apo -> mmcif", - "check modelled ligands", + "pre-run for ground state model", + "Build ground state model", + "------------------------------------------", + "pandda.analyse (PanDDA2)", ] xce_object.refine_file_tasks = [ From 1e8abed2d51bb9d874e72f24cc8774f71519ba3c Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 14:09:12 +0100 Subject: [PATCH 08/16] Update setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 29826470..fd08bd2e 100755 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name="xce", - version="2.0.1", + version="1.5.0", description="GUI tool for XChem", author="Tobias Krojer", packages=find_packages(), From ceef5617cf1986fe432788cff72a53a1416d9fcb Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 14:15:05 +0100 Subject: [PATCH 09/16] Update settings_preferences.py --- xce/gui_scripts/settings_preferences.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index 13e484a8..3a40854d 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -724,7 +724,11 @@ def dropdown_items(self, xce_object): ] xce_object.panddas_file_tasks = [ + "pre-run for ground state model", + "Build ground state model", + "------------------------------------------", "pandda.analyse", + "pandda.analyse (PanDDA2)", "pandda.inspect", "run pandda.inspect at home", "------------------------------------------", @@ -732,22 +736,18 @@ def dropdown_items(self, xce_object): "Export ALL PANDDA models", "Export SELECTED PANDDA models", "------------------------------------------", - "Show HTML summary", - "cluster datasets", - "Event Map -> SF", - "apo -> mmcif", - "check modelled ligands", - "------------------------------------------", "refine ALL bound-state models with BUSTER", "refine NEW bound-state models with BUSTER", "------------------------------------------", "refine ALL bound-state models with BUSTER (no sanity check)", "refine NEW bound-state models with BUSTER (no sanity check)", "------------------------------------------", - "pre-run for ground state model", - "Build ground state model", - "------------------------------------------", - "pandda.analyse (PanDDA2)", + + "Show HTML summary", + "cluster datasets", + "Event Map -> SF", + "apo -> mmcif", + "check modelled ligands", ] xce_object.refine_file_tasks = [ From 42afad4ca12ae5df70320fced52cb993c7b082c4 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 14:49:00 +0100 Subject: [PATCH 10/16] Update XChemRefine.py --- xce/lib/XChemRefine.py | 63 +++++++++++++++++++++++++----------------- 1 file changed, 37 insertions(+), 26 deletions(-) diff --git a/xce/lib/XChemRefine.py b/xce/lib/XChemRefine.py index 1e276e5c..3c3365f9 100755 --- a/xce/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -1070,17 +1070,17 @@ def RunRefmac( + "module load phenix/1.20\n" + "module load buster/20240123\n" + "module load ccp4\n" - + "cd " - + self.ProjectPath - + "/" - + self.xtalID - + "/Refine_" - + Serial + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + Serial + "\n" - + refinementStatus + + refinementStatus + "\n" + findTLS - + "refmac5 " + + "refmac5 " + RefmacParams["HKLIN"] + " " + RefmacParams["HKLOUT"] + " " + RefmacParams["XYZIN"] + " " @@ -1090,7 +1090,15 @@ def RunRefmac( + RefmacParams["TLSIN"] + " " + RefmacParams["TLSOUT"] + " " + "<< EOF > refmac.log\n" - + "make -hydrogen ALL -hout NO -peptide NO -cispeptide YES -ssbridge YES -symmetry YES -sugar YES -connectivity NO -link NO\n" + + "make -hydrogen ALL" + + "-hout NO " + + "-peptide NO " + + "-cispeptide YES " + + "-ssbridge YES " + + "-symmetry YES " + + "-sugar YES " + + "-connectivity NO " + + "-link NO\n" + RefmacParams["NCS"] + "refi -type REST -resi MLKF -meth CGMAT\n" + RefmacParams["BREF"] @@ -1100,23 +1108,26 @@ def RunRefmac( + RefmacParams["NCYCLES"] + "scal -type SIMP -LSSC -ANISO -EXPE\n" + weight + "solvent YES\n" - + "monitor MEDIUM -torsion 10.0 -distance 10.0 -angle 10.0 -plane 10.0 -chiral 10.0 -bfactor 10.0 -bsphere 10.0 -rbond 10.0 -ncsr 10.0\n" + + "monitor MEDIUM -torsion 10.0 -distance 10.0 -angle 10.0 -plane 10.0 " + + "-chiral 10.0 -bfactor 10.0 -bsphere 10.0 -rbond 10.0 -ncsr 10.0\n" + "labin FP=F SIGFP=SIGF FREE=FreeR_flag\n" - + "labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n" - + RefmacParams["TLSADD"] + + "labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT " + + "FOM=FOM\n" + + RefmacParams["TLSADD"] + "\n" - + "DNAME " + self.xtalID + + "DNAME " + self.xtalID + "\n" + "END\n" + "EOF\n" + "\n" + "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + "/bin/mv molprobity.out refine_molprobity.log\n" - + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n" % (Serial, Serial) - + "cd " - + self.ProjectPath - + "/" - + self.xtalID + + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz " + + "LIG > validate_ligands.txt\n" % (Serial, Serial)" + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + "\n" + "ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n" % (Serial, Serial) + "ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n" % (Serial, Serial) @@ -1133,18 +1144,18 @@ def RunRefmac( + "fft hklin refine.mtz mapout fofc.map << EOF\n" + "labin F1=DELFWT PHI=PHDELWT\n" + "EOF\n" - + "\n" - + updateDB + + "\n" + + updateDB + "\n" + "/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n" % (self.ProjectPath, self.xtalID) + "\n" - + "cd " - + self.ProjectPath - + "/" - + self.xtalID - + "/Refine_" + Serial + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + Serial + "\n" - + spider_plot + + spider_plot + "\n" ) From 3cc95d0e326aa88af31afc7af974ff570118d091 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 14:56:53 +0100 Subject: [PATCH 11/16] Update XChemRefine.py --- xce/lib/XChemRefine.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/xce/lib/XChemRefine.py b/xce/lib/XChemRefine.py index 3c3365f9..a55a06cf 100755 --- a/xce/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -1122,8 +1122,8 @@ def RunRefmac( + "\n" + "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + "/bin/mv molprobity.out refine_molprobity.log\n" - + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz " - + "LIG > validate_ligands.txt\n" % (Serial, Serial)" + + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG" + + " > validate_ligands.txt\n" % (Serial, Serial) + "cd " + self.ProjectPath + "/" From afb2ca73ff10cb7f7c7f139cd815b3efa90440f0 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 15:02:11 +0100 Subject: [PATCH 12/16] Update XChemRefine.py --- xce/lib/XChemRefine.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/xce/lib/XChemRefine.py b/xce/lib/XChemRefine.py index a55a06cf..92850c24 100755 --- a/xce/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -1122,8 +1122,8 @@ def RunRefmac( + "\n" + "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + "/bin/mv molprobity.out refine_molprobity.log\n" - + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG" - + " > validate_ligands.txt\n" % (Serial, Serial) + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG" + " > validate_ligands.txt\n" % (Serial, Serial) + "cd " + self.ProjectPath + "/" From 36830eea4795d14882fc9474a821e9f26fa71025 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 15:22:15 +0100 Subject: [PATCH 13/16] Update XChemRefine.py --- xce/lib/XChemRefine.py | 33 ++++++++++++++++++++++----------- 1 file changed, 22 insertions(+), 11 deletions(-) diff --git a/xce/lib/XChemRefine.py b/xce/lib/XChemRefine.py index 92850c24..1b54d470 100755 --- a/xce/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -1081,14 +1081,22 @@ def RunRefmac( + "\n" + findTLS + "refmac5 " - + RefmacParams["HKLIN"] + " " - + RefmacParams["HKLOUT"] + " " - + RefmacParams["XYZIN"] + " " - + RefmacParams["XYZOUT"] + " " - + RefmacParams["LIBIN"] + " " - + RefmacParams["LIBOUT"] + " " - + RefmacParams["TLSIN"] + " " - + RefmacParams["TLSOUT"] + " " + + RefmacParams["HKLIN"] + + " " + + RefmacParams["HKLOUT"] + + " " + + RefmacParams["XYZIN"] + + " " + + RefmacParams["XYZOUT"] + + " " + + RefmacParams["LIBIN"] + + " " + + RefmacParams["LIBOUT"] + + " " + + RefmacParams["TLSIN"] + + " " + + RefmacParams["TLSOUT"] + + " " + "<< EOF > refmac.log\n" + "make -hydrogen ALL" + "-hout NO " @@ -1107,7 +1115,8 @@ def RunRefmac( + "ncyc " + RefmacParams["NCYCLES"] + "scal -type SIMP -LSSC -ANISO -EXPE\n" - + weight + "solvent YES\n" + + weight + + "solvent YES\n" + "monitor MEDIUM -torsion 10.0 -distance 10.0 -angle 10.0 -plane 10.0 " + "-chiral 10.0 -bfactor 10.0 -bsphere 10.0 -rbond 10.0 -ncsr 10.0\n" + "labin FP=F SIGFP=SIGF FREE=FreeR_flag\n" @@ -1115,7 +1124,8 @@ def RunRefmac( + "FOM=FOM\n" + RefmacParams["TLSADD"] + "\n" - + "DNAME " + self.xtalID + + "DNAME " + + self.xtalID + "\n" + "END\n" + "EOF\n" @@ -1153,7 +1163,8 @@ def RunRefmac( + self.ProjectPath + "/" + self.xtalID - + "/Refine_" + Serial + + "/Refine_" + + Serial + "\n" + spider_plot + "\n" From 3671027ef51d7aefbccaf7fff2ccc7850b471a2c Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 15:22:54 +0100 Subject: [PATCH 14/16] Update settings_preferences.py --- xce/gui_scripts/settings_preferences.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index 3a40854d..3d3da8f1 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -1,12 +1,10 @@ import os import subprocess import sys - -from PyQt4 import QtCore - +import QtCore +from PyQt4 from xce.lib import XChemDB, XChemLog, XChemMain, XChemUtils - class setup: def __init__(self): pass @@ -742,7 +740,6 @@ def dropdown_items(self, xce_object): "refine ALL bound-state models with BUSTER (no sanity check)", "refine NEW bound-state models with BUSTER (no sanity check)", "------------------------------------------", - "Show HTML summary", "cluster datasets", "Event Map -> SF", From 3df159d7a898f5bac37a17a105d10faa43a6ba8d Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 15:27:19 +0100 Subject: [PATCH 15/16] Update settings_preferences.py --- xce/gui_scripts/settings_preferences.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index 3d3da8f1..ccd98448 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -2,9 +2,10 @@ import subprocess import sys import QtCore -from PyQt4 +from PyQt4 from xce.lib import XChemDB, XChemLog, XChemMain, XChemUtils + class setup: def __init__(self): pass From d4299915779f15f1262c604d18c5e2be786b0d78 Mon Sep 17 00:00:00 2001 From: Daren-fearon <64987111+Daren-fearon@users.noreply.github.com> Date: Thu, 1 Aug 2024 15:30:03 +0100 Subject: [PATCH 16/16] Update settings_preferences.py --- xce/gui_scripts/settings_preferences.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index ccd98448..5029ad20 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -1,8 +1,7 @@ import os import subprocess import sys -import QtCore -from PyQt4 +from PyQt4 import QtCore from xce.lib import XChemDB, XChemLog, XChemMain, XChemUtils