Individual steps explained (updated on 11/15/2016)
Step-#1: Select the virus entry that is in the database or upload the coordinates (in VIPER convention) of the virus particle.
If the user selected the existing entry in VIPERdb or the user uploaded the coordinates of an icosahedral asymmetric unit (IAU) (in the VIPER convention), then the full particle will be generated and used for the repositioning.
Step-#2: Select Yes or No, for the particle to be rotated by 90° around Z-axis from the VIPER orientation (to Purdue convention).
Step-#3: The user is asked to input the size of the box that the virus particle to be encased in (e.g., 400, 400, 400).
Step-#4: Click SUBMIT. A link to the coordinates will show up shortly.