How to run the GUI
The batch file C:\RECON5-3\RECON.BAT enables the WinRecon GUI to be run as a
single command from a DOS shell or from the Run dialog box in the Start Menu.
The batch file C:\RECON6-3\INSTALL.BAT compiles the java files. These file
assumes that java is located in the directory C:\jdk\bin
If you have installed java in a different directory, edit the C:\RECON5-3\RECON.BAT and C:\RECON6-3\INSTALL.BAT files to reflect the actual location of java.
recon6-3.exe can also be run without the GUI from a DOS shell or by double clicking the executable icon; if this option is used, the input is read from the file recon.inp in the C:\RECON6-3 directory.
The output summary files recon.ff (TAE descriptors), recon.stt (atom type visitation statistics) and recon.err (atom type mismatch log) are, by default, saved to the C:\RECON5-5 directory. Use the "Save As" option in the Notepad to save them elsewhere.
Note that the rpdb algorithm of the current version of recon5-5 requires ALL atoms (including Hydrogens) to be explicitly listed in the ATOM/HETATM records of the pdb file and ALL bonds to be explicitly listed in the BOND/CONECT records of the pdb file.
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