Merge pull request #50 from scipion-em/rm_fix_plot

show avg and std of all data not only the selected
scipion-em · Jun 4, 2021 · afd027a · afd027a
2 parents 6600cc2 + 3ed2447
commit afd027a
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Showing 2 changed files with 34 additions and 34 deletions.
diff --git a/phenix/protocols.conf b/phenix/protocols.conf
@@ -1,32 +1,32 @@
 [PROTOCOLS]
 Protocols SPA = [
-	{"tag": "section", "text": "Tools", "openItem": "False", "children": [
-	  {"tag": "protocol_group", "text": "Calculators", "openItem": "False", "children": [
-	    {"tag": "protocol", "value": "PhenixProtRunSuperposePDBs",   "text": "default"}
-	  ]}
-	]}]
+{"tag": "section", "text": "Tools", "openItem": "False", "children": [
+{"tag": "protocol_group", "text": "Calculators", "openItem": "False", "children": [
+{"tag": "protocol", "value": "PhenixProtRunSuperposePDBs", "text": "default"}
+]}
+]}]
 Model building = [
-	{"tag": "section", "text": "Imports", "icon": "bookmark.png", "children": [
-	]},
-	{"tag": "section", "text": "Preprocess map", "icon": "bookmark.png", "children": [
-	]},
-	{"tag": "section", "text": "Initial model", "icon": "bookmark.png", "children": [
-	]},
-	{"tag": "section", "text": "Rigid fitting", "icon": "bookmark.png", "children": [
-	{"tag": "protocol", "value": "PhenixProtRunDockInMap",   "text": "default"},
-	{"tag": "protocol", "value": "PhenixProtSearchFit",   "text": "default"}
-	]},
-	{"tag": "section", "text": "Flexible fitting", "icon": "bookmark.png", "children": [
-	{"tag": "protocol", "value": "PhenixProtRunRSRefine",   "text": "default"}
-	]},
-	{"tag": "section", "text": "Validation", "icon": "bookmark.png", "children": [
-	{"tag": "protocol", "value": "PhenixProtRunEMRinger",   "text": "default"},
-	{"tag": "protocol", "value": "PhenixProtRunMolprobity",   "text": "default"},
-	{"tag": "protocol", "value": "PhenixProtRunValidationCryoEM",   "text": "default"}
-	]},
-	{"tag": "section", "text": "Tools-Calculators", "icon": "bookmark.png", "children": [
-	{"tag": "protocol", "value": "PhenixProtRunSuperposePDBs",   "text": "default"}
-	]},
-	{"tag": "section", "text": "Others", "icon": "bookmark.png", "children": [
-	]}
-	]
+{"tag": "section", "text": "Imports", "icon": "bookmark.png", "children": [
+]},
+{"tag": "section", "text": "Preprocess map", "icon": "bookmark.png", "children": [
+]},
+{"tag": "section", "text": "Initial model", "icon": "bookmark.png", "children": [
+]},
+{"tag": "section", "text": "Rigid fitting", "icon": "bookmark.png", "children": [
+{"tag": "protocol", "value": "PhenixProtRunDockInMap", "text": "default"}
+]},
+{"tag": "section", "text": "Flexible fitting", "icon": "bookmark.png", "children": [
+{"tag": "protocol", "value": "PhenixProtRunRSRefine", "text": "default"},
+{"tag": "protocol", "value": "PhenixProtSearchFit", "text": "default"}
+]},
+{"tag": "section", "text": "Validation", "icon": "bookmark.png", "children": [
+{"tag": "protocol", "value": "PhenixProtRunEMRinger", "text": "default"},
+{"tag": "protocol", "value": "PhenixProtRunMolprobity", "text": "default"},
+{"tag": "protocol", "value": "PhenixProtRunValidationCryoEM", "text": "default"}
+]},
+{"tag": "section", "text": "Tools-Calculators", "icon": "bookmark.png", "children": [
+{"tag": "protocol", "value": "PhenixProtRunSuperposePDBs", "text": "default"}
+]},
+{"tag": "section", "text": "Others", "icon": "bookmark.png", "children": [
+]}
+]
diff --git a/phenix/viewers/viewer_search_fit.py b/phenix/viewers/viewer_search_fit.py
@@ -69,9 +69,9 @@ def _defineParams(self, form):
         form.addParam("numAtomStruct", IntParam, label="Max. Number Atom Structs.",
                       default=1000,
                       help="Number of atom structs to show ordered by model_to_map_fit\n")
-        form.addParam("zone", FloatParam, label="Show Area arround input PDB (A)",
+        form.addParam("zone", FloatParam, label="Show Area around input atomic struct (A)",
                       default=3,
-                      help="Limit the display to a zone around the input PDB.\n"
+                      help="Limit the display to a zone around the input atomic structure.\n"
                            "Units = A.")
         form.addParam('showPlot', LabelParam,
                       label="Summary Plot",
@@ -182,15 +182,15 @@ def _showPlot(self, e=None):
                              FROM %s
                              WHERE model_to_map_fit != -1
                              ORDER BY model_to_map_fit desc
-                             LIMIT %d)""" % (TABLE, self.numAtomStruct)
+                             )""" % (TABLE)
         c.execute(sqlCommand)
         rows = c.fetchone(); avg = rows[0]
         print("avg", avg)
         fromRelation = """(SELECT model_to_map_fit
                              FROM %s
                              WHERE model_to_map_fit != -1
                              ORDER BY model_to_map_fit desc
-                             LIMIT %d) AS mainTable""" % (TABLE, self.numAtomStruct)
+                             ) AS mainTable""" % (TABLE)
 
         sqlCommand = """SELECT AVG((mainTable.model_to_map_fit - sub.a) * (mainTable.model_to_map_fit - sub.a)) as var
                         FROM %s,
@@ -210,7 +210,7 @@ def _showPlot(self, e=None):
             errorWindow(self.getTkRoot(), "No data available")
             return
 
-        title = 'Map Model Fit - avg = %f, std = %f'%(avg, std)
+        title = 'avg (all data) = %f, std (all data) = %f'%(avg, std)
         plt.plot(xList, yList, 'x')
         plt.axis([0, max(xList) + 1.0, 0.0, max(yList)+0.1])
         plt.title(title)