How to use the Oligomer Generator

Individual steps explained (updated on 11/15/2016)

  • Step-#1: Select a viral capsid -OR- Upload your coordinates PDB formatted file in the VIPERdb convention.

    **NOTE: the coordinates MUST be in VIPERdb convention for the oligomer generator to work properly!

  • Step-#2: If you would like to generate either the complete capsid or a given section of the capsid (e.g., full or half), simply select the corresponding oligomer from the pull-down menu. Then skip ahead to the bottom and click SUBMIT. A link to the oligomer (coordinates) will show up shortly.

  • Step-#3: If you like to generate an Oligomer of your Choice, select the T number of your virus capsid from the menu (T numbers are listed at the end of the capsid name; see Step1)
    When you select the T number, corresponding lattice diagram should appear in this panel.

    Enter the labels of the subunits you would like generated (A1, C2, etc.) or asymmetric unit numbers (1, 2, 3, etc.) as they are shown in the lattice diagram.

  • Step-#4: If you would like to include only use the C-alpha atoms in the oligomer, choose 'YES', the default is no, all the atoms will be included in the oligomer generation .

  • Click SUBMIT. A link to the oligomer (coordinates) will show up shortly.