If the flag ASSIGN_DELOCALIZED in config.dat is set to 1, the ligand formal charges are delocalised automatically, i.e., in the carboxylate example above, both oxygen atoms receive a formal charge of -0.5 and, thus being symmetric, no 180° rotation will be performed. The default setting though is 0, i.e., no alterations to the input settings are made.

Our recommendation is: Examine your input file to be really sure which charges are present and choose the appropriate mode for ASSIGN_FORMAL_CHARGES and ASSIGN_DELOCALIZED.

New in Release 2:
The delocalisation, among others, is now handled by a new parameter, USE_TRANSFORMS in config.dat. If USE_TRANSFORMS is set to 1, the ligand passes through several levels of initialisation, which in turn are specified in a new static_data file, transform.dat:

Level 1		Correct valences and bonds in PDB structures [OFF]
Level 2		Preprocess / localize molecule [ON]
Level 3		Aromaticity check [ON]
Level 4		Assign default protonation [ON]
Level 5		Assign formal charges [ON]
Level 6		Assign delocalized systems [ON]
Level 10		Assign atom-types [ON]

The flag ASSIGN_DELOCALIZED is still kept for backwards compatibility, but will be removed in one of the following versions of FlexX. For the time being, the flag still has to be set to 1 in the config.dat, together with USE_TRANSFORMS in order to invoke the delocalisation, but this can also be controlled from the command line under the LIGAND submenu in FlexX as shown below. The setting in the config.dat file will then be overwritten.

Type 'SELINIT' and then the number of the level you would like to turn on, or 'SELINIT !' and the number of the level you would like to turn off. E.g. 'SELINIT 6' would turn on, 'SELINIT !6' would turn off the delocalisation.