TIPs

Tips for "best-practices" in using ProtDCal:

• Increase the memory for the Java Virtual Machine, while launching ProtDCal's graphical user interface. An example for using 2000MB is as follow: java -Xmx2000m -jar ProtDCal.jar


• Save project files to keep a record of your calculations.


• Use properly formated PDB files:
  • Check the presence of lines TER, END or ENDMDL.
  • Secundary structure-based groups (SHT, HEX, TRN, RCL) require the explicit definition of secundary structure ranges in the PDB files.
  • Backbone's hydrogens should be present to compute the indices Hbd and wDHbd.


• Use the 'Run Multi-project' tool in the GUI in order of executing several project files in batch mode.


• Use the Perl script ProtDCal-parallel.pl to run parallel calculations using ProtDCal. Options can be learn from a README-parallel.txt file by excecuting: perl ProtDCal-parallel.pl -h


• Use the command line interface to execute ProtDCal.jar or ProtDCal-parallel.pl for the next objectives:
  • Multiproject calculations
  • User-specified descriptors calculations (IDL projects)
  • Protein-protein interactions descriptors


• Option for the command line interface appears in the Readme_vx.txt file and the manual as well as in the README file with the help of the Perl script.