[PyMOL] Electron density map carving issue

[Mehmet G. <mg...@ku...>]

I am trying to create figures showing only the ligand with electron density
using an mtz file. The commands I am using to create the density map are as
follows:
map_double h.map
select local,resn GEN
isomesh map,h.map,1.0,local,carve=2.5

It works fine for one structure but I am having an issue for the others.
The issue is that the density around the ligand has gaps at both ends of
the molecule, instead of covering it entirely. I am attaching two figures
showing the difference. Thank you in advance for your help.

[image: c1_local.png][image: siso_local.png]