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 1.7.2.0
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 )
Sincerely,
Justin T. Biel
Graduate Student
University of California San Francisco
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