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The structure was manually modified to fit into the electron density maps, using the program Coot44, and then refined with the programs Phenix43 and Refmac5 in the CCP4 suite45.
The resulting response is shown to be fast and stable in comparison to previous designs which used fixed fuzzy logic antecedents that need to be manually modified whenever the environmental conditions change or if a different solar panel is used.
If an error is detected, the program or the model is manually modified and verified again.
The alignments were manually modified to correct defects from the automatic alignment method of ClustalW.
The thickness of the layers used for the fundamental parameter calculations is manually modified by the user until good agreement between simulation and measurement is achieved.
It also provides facilities to depict reaction mechanisms and schemes; structures generated with mol2chemfig can be manually modified and incorporated into such schemes.
The initial sequence alignments were manually modified based on structural alignments and superimpositions of coordinates of the homologous GPCRs using DS3.5.
Nevertheless, using parametric smart objects libraries can be slightly restrictive, since if a specific architectural style is not present in parametric libraries, they need to be manually modified.
The alignments were manually modified to improve validation results, and the modelling and validation processes repeated until models with good geometry and conformations were obtained.
To facilitate system maintenance and reconfiguration, all the correctly configured options can be saved to a text file, which can be manually modified as required.
The resulting alignments were manually modified using BioEdit program (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
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