 | | |
| Command | | Argument |
| Datatype | | Default | | Min | | Max |
| | | Format: | | CorrectConv | | Type = On
| Off | | STRING |
| - |
| - | | - | |
| | Python: | | CorrectConv(Type) |
| | | Menu: | | Simulation > Automatic correction of > wrong naming conventions | | |
| | Related: | | CorrectIso, CorrectCis
| | | |
| Required: | |  | |
|
The CorrectConv
command toggles the enforcement of atom naming conventions during a simulation. If an unrealistic simulation is run at high temperature
(for example simulated annealing runs for NMR structure determination), pairs of atoms can change place. The result can be serious errors in the structure
( cis-peptide bonds or wrong stereoisomeres
, as well as simple deviations from naming conventions. Since atom names are just labels attached by humans,
YASARA ignores them whenever possible, but especially NMR spectroscopists often rely on them when assigning stereo-specific restraints. If set to
'On', the CorrectConv command therefore detects and corrects the following naming problems by swapping the atoms back:
The corrections stay in effect until either the command
'CorrectConv Off' or 'Reset' is issued. While methylene,
amide and guanidine corrections also consider unusual amino acids, the correction of methyl groups in Val and Leu
relies on correct residue and atom names to function properly.
Example 1:
CorrectConv On
Correct deviations from various atom naming conventions during a simulation.
Example 2:
CorrectConv Off
Do not correct naming conventions during a simulation.
| 
