I am very sorry for bothering the list members with my previous email. I figured this myself, I just need to "reset" from the command line. Sincerely, Vis To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Sent: Thursday, September 20, 2012 12:25 PM Subject: solvation box transformed Dear Users, I have some difficulties with reference frames when solvating a protein. The essence of my problem as follows. Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop, it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not allow to transfer the inpcrd coordinates to another program (NAMD). Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool? Sincerely, Vis