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Fix for HKLIN and XYZIN issue in refmac refinement #426

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merged 18 commits into from
Aug 1, 2024
Merged

Fix for HKLIN and XYZIN issue in refmac refinement #426

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00535a4
Update XChemRefine.py
Daren-fearon Aug 1, 2024
c40f609
Update setup.py
Daren-fearon Aug 1, 2024
a8246c3
Merge pull request #1 from Daren-fearon/Daren-fearon-patch-20240801
Daren-fearon Aug 1, 2024
cbf66ef
Merge pull request #2 from Daren-fearon/Daren-fearon-patch-20240801-1
Daren-fearon Aug 1, 2024
9988e07
Update settings_preferences.py
Daren-fearon Aug 1, 2024
debf9b2
Update XChemLog.py
Daren-fearon Aug 1, 2024
517717b
Update XChemLog.py
Daren-fearon Aug 1, 2024
3036241
Update settings_preferences.py
Daren-fearon Aug 1, 2024
ae09863
Update settings_preferences.py
Daren-fearon Aug 1, 2024
1e8abed
Update setup.py
Daren-fearon Aug 1, 2024
ceef561
Update settings_preferences.py
Daren-fearon Aug 1, 2024
42afad4
Update XChemRefine.py
Daren-fearon Aug 1, 2024
3cc95d0
Update XChemRefine.py
Daren-fearon Aug 1, 2024
afb2ca7
Update XChemRefine.py
Daren-fearon Aug 1, 2024
36830ee
Update XChemRefine.py
Daren-fearon Aug 1, 2024
3671027
Update settings_preferences.py
Daren-fearon Aug 1, 2024
3df159d
Update settings_preferences.py
Daren-fearon Aug 1, 2024
d429991
Update settings_preferences.py
Daren-fearon Aug 1, 2024
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23 changes: 10 additions & 13 deletions xce/gui_scripts/settings_preferences.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,7 @@
import os
import subprocess
import sys

from PyQt4 import QtCore

from xce.lib import XChemDB, XChemLog, XChemMain, XChemUtils


Expand All @@ -23,7 +21,7 @@ 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
Expand Down Expand Up @@ -724,30 +722,29 @@ 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",
"------------------------------------------",
"Export NEW PANDDA models",
"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 = [
Expand Down
5 changes: 1 addition & 4 deletions xce/lib/XChemLog.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
" # [email protected] #\n"
" # Date: 01/08/2024 #\n"
" # #\n"
" ###################################################################\n"
"\n" % pasteVersion
Expand Down
124 changes: 64 additions & 60 deletions xce/lib/XChemRefine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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",
)

#######################################################
Expand Down Expand Up @@ -1069,69 +1069,68 @@ def RunRefmac(
+ '"\n'
+ "module load phenix/1.20\n"
+ "module load buster/20240123\n"
+ "module load ccp4\n"
+ "cd "
+ self.ProjectPath
+ "/"
+ self.xtalID
+ "/Refine_"
+ Serial
+ "\n"
"\n"
+ 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"
+ " "
+ "<< 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)
Expand All @@ -1140,30 +1139,35 @@ def RunRefmac(
+ "/"
+ 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):
Expand Down
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