[PyMOL] Cryo Maps - gaussian isosurface

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,

[PyMOL] shadows commands

Hi All, I’m trying to write scripts that include shadow options. In the menus at the top of the program users can choose: Setting/Rendering/Shadows and then they can pick: None, light, medium, heavy, black, matte, soft, occlusion 1, and occlusion 2. How do I put those shadows into a script?

Re: [PyMOL] shadows commands

> <http://www.bioc.uzh.ch/plueckthun/antibody> > http://www.bioc.uzh.ch/plueckthun/nanowelt > <http://www.bioc.uzh.ch/plueckthun/nanowelt> > > > >> On 06 Apr 2016, at 05:57, pymol-users-requ...@lists.sourceforge.net >> <mailto:pymol-users-requ...@lists.

Re: [PyMOL] pymolrc location

n .pymolrc, creating the file if > it doesn't exist. > > Cheers, > Jared > >> On Apr 8, 2016, at 11:42 AM, harold steinberg <h.adam.steinb...@gmail.com >> <mailto:h.adam.steinb...@gmail.com>> wrote: >> >> Sorry to be inept… I've never had the opportun

Re: [PyMOL] pymolrc location

where in OS X is pymolrc located? > On Apr 7, 2016, at 2:39 PM, Thomas Holder > wrote: > > pymolrc H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 --

Re: [PyMOL] pymolrc location

all <li...@cowsandmilk.net> wrote: > > Make a file at ~/.pymolrc > > -David > >> On Apr 8, 2016, at 10:35 AM, harold steinberg <h.adam.steinb...@gmail.com> >> wrote: >> >> where in OS X is pymolrc located? >> >>> On Apr 7, 2016,

Re: [PyMOL] Cryo Maps - gaussian isosurface

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

[PyMOL] color an isosurface with a rainbow

I have a pdb ‘xyz1’ and create a mapA, then create a surfA. set surface_quality, 1 alter all, b=50 alter all, q=1 set gaussian_resolution,5 map_new mapA, gaussian, 1, sele or pdb, 6 isosurface surfA, mapA I can then color that surfA with any solid color. How can one color the surfA with a

[PyMOL] movies - transparency?

Hi all, 1. If I set a surface with 70% transparency and then generate a morph of it - all looks great. However, when I save a movie of that morph the transparent surface turn almost solid, though you can still see the cartoon backbone (looks more like 5% transparency). Is there anyway to

Re: [PyMOL] morph issues

I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session. > On Apr 26, 2016, at 6:16 AM, harold steinberg <h.adam.steinb...@gmail.com> > wrote: > > Hi Annemarie, > > Thank you for the answer. Do you know the comm

Re: [PyMOL] morph issues

ioc.uzh.ch/plueckthun/antibody > <http://www.bioc.uzh.ch/plueckthun/antibody> > http://www.bioc.uzh.ch/plueckthun/nanowelt > <http://www.bioc.uzh.ch/plueckthun/nanowelt> > > > > > > >> On 26 Apr 2016, at 13:21, harold steinberg <h.adam.steinb...@gma

Re: [PyMOL] morph issues

; sort > > # illustrate that the order is the same now: > > spectrum segi > label guide and resn ALA, segi > > # Now the morphing should work as expected: > > morph mout, 3j5r, 3j5q, refinement=0 > > Hope that helps. > > See also: > http://pymolwiki.org/

[PyMOL] morph issues

Hi all, I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it’s all messed up. When I generate a morph of other structures it works just fine. In the structures that do not morph correctly a sample selection is: /3j5r/A/B/ILE`573/CD1

Re: [PyMOL] High Resolution Ray Tracing

The 9600 x 4800 is a very common poster printer spec. Most print shops use 180 dpi images on their poster printers (for best print speed) and customers cannot tell the difference between that and a higher resolution. As a test, render a small image (say 6” x 6”) in PyMOL at four different dpi,

Re: [PyMOL] High Resolution Ray Tracing

rtcut for creating the 6" test > images: > > png image1.png, 6in, ray=1, dpi=180 > png image2.png, 6in, ray=1, dpi=300 > png image3.png, 6in, ray=1, dpi=600 > png image4.png, 6in, ray=1, dpi=1200 > > Cheers, > Thomas > > On 10 May 2016, at 14:27, harold

Re: [PyMOL] Iterate scenes smoothly

that’s the same result I always get… > On May 9, 2016, at 12:23 PM, Leandro Bortot wrote: > > Dear users, > > I'm trying to make a movie during which a surface changes its color. I > followed the tutorials from the wiki and successfully created two scenes with >

Re: [PyMOL] High Resolution Ray Tracing

I can try to address the 2400 dpi printer resolution. Printer manufactures specify their printer's resolution in the number of pixels per inch (ppi) in the horizontal plane because it’s higher, and looks better in advertising. But all printers also have a vertical printing resolution that is

Re: [PyMOL] Color residue in cartoon mode

I believe that you can only apply the cartoon setting to an entire obj (object). And so you are correct in trying to duplicate the nucleotide so you can apply one setting to it, while allowing the other setting to display the rest of them. But that doesn’t work either since the program will

Re: [PyMOL] Color residue in cartoon mode

ring_mode" for the > residue selection. Example: > > fetch 1rna, async=0 > as cartoon > select firstres, chain A & resi 1 > set cartoon_ring_finder, 2 > set cartoon_ring_mode, 2, firstres > color blue > color red, firstres extend 1 > > Hope that helps.

Re: [PyMOL] issues presenting DNA

You can change the color of the tube backbone with "set cartoon_nucleic_acid_color, blue”. But it’s my understanding that the color of the backbone is always set to only one color. You cannot make part of it one color and part of it another color. If you try you’ll get the following warning:

Re: [PyMOL] issues presenting DNA

Wow that is unintuitive. But it does indeed work! > On Sep 6, 2016, at 2:33 PM, Paul Paukstelis wrote: > > David, > > I'm pretty sure that all you have to do is change the color of individual > phosphorous atoms to change the tube backbone color. > > --paul > > >