Thank you Thomas, that certainly works, but it’s not as smooth as Chimera. I took a bit of a crash course in Chimera and figured out how to gaussian the map and then export it as a .mrc file. I could then open that in PyMOL and proceed!
> On Apr 8, 2016, at 2:56 PM, Thomas Holder <thomas.hol...@schrodinger.com> > wrote: > > Hi Adam, > > As I understand, you want to do some low-pass smoothing on the map, correct? > I'm not aware that this functionality would be available in PyMOL. However, > PyMOL can downsample the map, which averages 8 voxels into 1 and thus also > provides some level of smoothing. Try this: > > fetch emd_6413, map, async=0 > map_halve map > map_halve map > isomesh mesh, map > > Hope that helps. > > Cheers, > Thomas > > On 05 Apr 2016, at 15:24, harold steinberg <h.adam.steinb...@gmail.com> wrote: > >> Hi All, >> >> I’m trying to make an isomesh of EMD-6413 (a cryo map) in Pymol. It’s a >> large map with a lot of extra, not very clean. In Chimera I can just >> gaussian the map with a new map to the level I want with a slider and it >> looks good, but I’d much rather work in PyMOL! >> >> PyMOL can gaussian maps, I do it all the time, but on maps that I create in >> PyMOL. How do I get an isomesh on EMD-6413 that I can gaussian? >> >> Normally I would use: >> alter all, q=1 >> set gaussian_resolution, 5 >> map_new mapA, gaussian, 1, pdb code, 6 >> isosurface surfA, mapA >> >> But in in this case I don’t want to use a pdb, just the cryo map. >> >> I can isosurface the cryo map with the following: >> isosurface mapname, EMD-6413, 4 (any number between 1-6) >> >> but that doesn’t allow me to apply the gaussian to the map… >> >> How do I create an isosurface with a gaussian? >> >> Thanks for any help, >> >> H. Adam Steinberg >> 7904 Bowman Rd >> Lodi, WI 53555 >> 608/592-2366 > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 ------------------------------------------------------------------------------ Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/ gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532 _______________________________________________ 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
