diff --git a/modules/io/doc/profile.rst b/modules/io/doc/profile.rst index bb6d41e27bf34d592acd403f05c1793de2721427..9ab8a395cc0e6b99d583fd2eff1dabfcab25d1d9 100644 --- a/modules/io/doc/profile.rst +++ b/modules/io/doc/profile.rst @@ -151,14 +151,15 @@ The IOProfile Class :type: bool - Only relevant when reading PDB format. When set to true, reads CONECT - statements and applies them in the pdb reader. This can result in - hydrogen bonds salt bridges etc. to be connected. Check the PDB format - definition for more info. This may cause issues in subsequent processing - with the processor as we suddenly have two places where connectivity is - built. For the use case of valid CONECT statements for all hetatms, you - may want to disable processing of bonds between them in - :attr:`ost.conop.Processor.connect_hetatm` + Only relevant when reading files in PDB format. When set to true, reads CONECT + statements and applies them in the PDB reader. This can result in + hydrogen bonds, salt bridges etc. to be connected. Check the PDB format + definition for more info. This may cause issues in subsequent processing, + such as bonds being overriden, or extra, inconsistent bonds, as the + processor suddenly has two separate sources of connectivity. + For the use case where the input PDB file contains valid CONECT + statements for all hetatms, you may want to disable processing of bonds + between them in :attr:`ost.conop.Processor.connect_hetatm` .. attribute:: processor