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Article ID: 437 - Last Modified: April 30, 2012

I notice there is a "phantom residue" that appears right next to a normal, regular residue. While the normal residue can be manipulated the phantom residue cannot. Why is it appearing and what is the point of it?

The "phantom residue" is an alternate conformation of the structure. You can display and undisplay alternate conformations with Workspace → Alternate Positions (from Suite 2010) or Display → Alternate Positions (earlier releases). If you do not want to read alternate coordinates when you import a PDB file, deselect the option "For PDB files, read alternate locations".

If you want to adjust the position of the alternate conformation, select the residue and choose Switch Alternate Positions from the selection context menu (right-click and hold in the Workspace). If you are doing local transformations on the main conformation and you want to also transform the alternate conformation, select "Include alternate positions in local transformations" in the Preferences panel, under Workspace → Transformations (Suite 2011 on) or the Workspace tab (Suite 2010).

Keywords: alternate positions, alternate conformations, Maestro

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