Vilualizing solvent distribution
Dear all, I want to visualize solvent(water) distributions around one solute molecule. I do molecular dynamics calculation with Amber8 program. So I got the following ouput file using grid command of Ptraj module to analyze trajectories. This line is ignored 1 rdparm generated grid density 100 -49 50 100 -49 50 100 -49 50 30.000 30.000 30.000 90.000 90.000 90.000 ZYX -49 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 I think the output is in the format of a XPLOR formatted contour file and can visualize this output data within chimera soft ware. But I don't know how to treat this out put file in chimera . Can I use this file directory in chimera or have to do anything else before I use chimera? Thanks Atsutoshi
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: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht... Tom
participants (2)
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Atsutoshi Okabe -
Thomas Goddard