As is usual with mysterious "permission denied" errors, SELinux was the underlying cause. ...
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as
ID Status▲ Resolution Sev Product Comp Assignee▲ Reporter Summary
13145 CLOS FIXE nor Sisyphus chemtool mike sbolshakov weird desktop file pathname
15636 CLOS FIXE nor Sisyphus chemtool mike solntsev Патч, позволяющий дописывать расширения *.cht к именам файлов, которые уже зарегистрированы в системе.

File a new bug in the "chemtool" component of the "Sisyphus" product