Hi Andrés, There are many possible ways. One way would be to select only the water molecules you want to keep and then use the command: delete solvent & ~sel (delete solvent that is not selected). You can show the command line using the Favorites menu, and select with the mouse as described here <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect> ...or with a command, for example select :445.A,480.A Since you only want to keep a few and delete many, this approach is probably easier than selecting or listing all the ones you wanted to delete. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 21, 2013, at 8:57 AM, felipe vasquez wrote:

Hi, I am trying to prepare a protein structure for docking, and I want to keep just one or a couple of water molecules. How can I do achieve this goal, deleting the rest of solvent molecules? Thanks in advance. Best regards, Andrés Felipe Vásquez J., MSc. Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia