Dear all, We released PyMOL 1.7.2.1 which fixes the volume carving issue that was reported by Justin (see below). The Incentive PyMOL installers (http://pymol.org/download ), as well as the open-source SVN code (rev 4087) have been updated.
Cheers, The PyMOL Team at Schrödinger On 06 Aug 2014, at 16:48, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > 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. ------------------------------------------------------------------------------ _______________________________________________ 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
