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Re: [PyMOL] Cryo Maps - gaussian isosurface
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From: harold s. <h.a...@gm...> - 2016-04-10 04:02:33
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> On Apr 8, 2016, at 5:34 PM, harold steinberg <h.a...@gm...> wrote: > > 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 <tho...@sc...> 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.a...@gm...> 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 > H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
