Dear Yanming,
To show "pretty" density of a model you have to import a ccp4 density
map and display it around your ligand. The simplest solution is using
ccp4 and tick the box "Generate weighted difference maps files in CCP4
format" when running Refmac5 (one or two cycles are enough). Specify
names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4.
This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density
around our ligand you can use the following command:
isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8
("map" = greats an object name map, "name_of_fwtmap" = name of your map,
"1.0" = Sigma level, "carve=1.8" = width map is displayed around your
ligand
This will allow you to show a "pretty" electron density map around your
ligand without any chemical info of the ligand.
Stefan Schmelz
Yanming Zhang wrote:
Hi, all,
I want to make a pymol figure wich can show the pretty density of a
ligand. But we don't want to show the detailed chemical info of the
ligand. If I use a large enough sphere_scale for the ligand, the
chemical info will be hidden but the density map will be disrupted. If
I use a smaller sphere_scale, the density looks great but the chemical
info of the ligand will be visible. How should I overcome this dilemma?
Thank you very much for your help.
Yanming
