Operating systems: MacOS and Linux.

Contacts : Nuno Sousa Cerqueira

VMD is an exceptional program to visualize molecular structures. The main drawback of this software is the learning curve that turns it hard to use by non-expert users. One of the major difficulties that non-expert users have while handling VMD regards the selection of atoms. This is done through a series of keywords that the user must dominate in order to for example visualize and/or hide particular parts of the molecule, do specific transformations on the atoms of that selectin, etc.

In order to overcome this issues we have developed “Selection Manager”. This plug-in allows to do common selections on molecules without requiring any prior knowledge regarding the keywords available on VMD. It makes the selection of atoms simpler and easy for non-expert users. In addition it still allows the insertion of advanced commands but alerts the user for any error that might exist on the syntax.

In order to run the”Selector Manager” plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ .

The selector manager plug-in can be installed in any operating systems where VMD works. In order to work the user has to add the following lines to the .vmdrc that can be found on the home directory:

   #### selectionMAnager
   lappend auto_path /home/users/nunocerqueira/selectionManager
   vmd_install_extension selV "::selV::start"  "PortoBioComp/Selection Manager"
   ## END 

Note: /home/users/nunocerqueira/selectionManager is the directory where the plug-in has been installed.

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