[Chimera-users] Vilualizing solvent distribution

Thomas Goddard goddard at cgl.ucsf.edu
Wed Oct 11 09:43:02 PDT 2006

Hi Atsutoshi,

  You should be able to open the XPLOR format file using Chimera menu
entry File / Open....  If the file name ends in ".xplor" it will be
opened in XPLOR format.  Or if it has a different file suffix you
can choose "all (ask type)" from the File / Open dialog "File type"
menu, then open the file and you will be asked to identify the file
type from a list.  Choose "CNS or XPLOR density map".

  Opening the file will display it as a contour surface using the
volume viewer tool.  You may want to switch to "solid" display style
in the volume dialog.  By moving the square nodes on the data histogram
in the volume dialog you can adjust brightness and control what map
values are displayed.

  Chimera can also directly compute occupancy of water or ions from an
MD trajectory.  See the "occupancy analysis" section of the Chimera MD Movie
tool documentation:



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