I am experiencing a problem with representing negative difference density with the volume representation. When I display the volume, it not only show signal where I would expect based on isomesh at the same contour level, but it also show signal at the edge of where I am carving around the molecule.

I am running pymol version

Here is some script that can be used to illustrate the problem I am having, or perhaps show what I am doing incorrectly.

bg white
set normalize_o_maps, 0
fetch 4bs0A, async=0
fetch 4bs0, dmap_4bs0, type=fofc, async=0
hide everything
show car, resi 126-128
car loop
select D127, resi 127
show sticks, (n. ca or sc.) and D127
hide sticks, hydrogens
set stick_radius, 0.10
isomesh fofc_neg, dmap_4bs0, -0.25, resi 127, carve=1.5
set mesh_color, red, fofc_neg
volume_ramp_new neg_ramp, \
-0.26 red 0. \
-0.25 red 1. \
-0.24 red 0. 
volume neg_vol, dmap_4bs0, neg_ramp, selection=D127, carve=1.5
set_view (\
    -0.487582058,    0.864638865,   -0.121075086,\
    -0.439162642,   -0.123027928,    0.889938176,\
     0.754581511,    0.487090826,    0.439703643,\
     0.000163982,    0.000030157,  -17.993944168,\
    16.466907501,   -2.307159424,  -22.514865875,\
    13.251377106,   22.765058517,  -20.000000000 )

Justin T. Biel
Graduate Student
University of California San Francisco