Hi Justin, this is a good find, and clearly illustrated by your script (I wish all bug reports would come with such a script!). I looked into this and found that PyMOL, when it carves out the selection, sets all the masked map voxels to the minimum map value. This can't be right, at least not for data which follows a normal distribution. Setting those voxels to the mean value, or even better, introduce a user-controllable setting (with default 0.0) makes more sense. We can fix that in the next minor release.
Cheers, Thomas On 06 Aug 2014, at 15:26, Biel, Justin <justin.b...@ucsf.edu> wrote: > 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 -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
