> I just download PYMOL into my Linux and it's working very nicely but I > want to check > whether it is possible to move a pdb file within a 3D density map > independently to get a > best fitting.
Yes, you can move the molecule, but not the map. First, get into editing mode: edit_mode (or select 3 Button Editing Mode from the Mouse menu, if you have one) Then, to move the whole molecule: shift-middle-click-and-drag on the molecule to translate shift-left-click-and-drag on the molecule to rotate ctrl-shift-middle-click on an atom to reset origin of rotation To rotate bonds, Ctrl-right-click-and-drag. Always click on the "mobile" side of the bond, otherwise, you'll end up moving the wrong portion of the molecule. To write out the new coordinates... save file.pdb, object-name NOTE: some of the above is specific to version 0.90, so make sure that's the version you have. Cheers, Warren