Correction for bond_dist program outputting bond_dist.log - not bond_dist.err

Ezra Peisach · Ezra Peisach · commit 982782c3e635 · 2026-03-27T11:30:27.000-04:00
diff --git a/wwpdb/utils/dp/RcsbDpUtility.py b/wwpdb/utils/dp/RcsbDpUtility.py
@@ -4100,7 +4100,7 @@ def __rcsbStep(self, op):
                 link_radii = self.__inputParamDict["cc_link_radii"]
                 cmd += " -link_radii " + link_radii
             cmd += " > " + tPath + " 2>&1 ; cat " + tPath + " >> " + lPath
-            cmd += " ; cat bond_dist.err" + " >> " + lPath
+            cmd += " ; cat bond_dist.log" + " >> " + lPath
         elif (op == "chem-comp-assign") or (op == "chem-comp-assign-skip") or (op == "chem-comp-assign-exact"):
             # set up
             #

Original file line number	Diff line number	Diff line change
`@@ -4100,7 +4100,7 @@ def __rcsbStep(self, op):`
`4100`	`4100`	`link_radii = self.__inputParamDict["cc_link_radii"]`
`4101`	`4101`	`cmd += " -link_radii " + link_radii`
`4102`	`4102`	`cmd += " > " + tPath + " 2>&1 ; cat " + tPath + " >> " + lPath`
`4103`		`- cmd += " ; cat bond_dist.err" + " >> " + lPath`
	`4103`	`+ cmd += " ; cat bond_dist.log" + " >> " + lPath`
`4104`	`4104`	`elif (op == "chem-comp-assign") or (op == "chem-comp-assign-skip") or (op == "chem-comp-assign-exact"):`
`4105`	`4105`	`# set up`
`4106`	`4106`	`#`