I'd be curious to know if there is any consensus in the community with using the "carve" command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map.
The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html "If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms." Just curious, Andy -- Andrew M. Gulick, Ph.D. ----------------------------------- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 ----------------------------------- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, "Stefan Schmelz" <[EMAIL PROTECTED]> wrote: > 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
