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
>
>
>
> On 09/05/2016 10:58 PM,
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: 'c
sidue 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.
>
> Cheers,
> Thomas
&
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 only
> 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 steinberg wrote:
>
>> The
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,
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
mu
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
> the desired colors.
>
; 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
tibody
> <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 > <mailto:h.adam.steinb...@gmail.com>>
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
> wrote:
>
> Hi Annemarie,
>
> Thank you for the answer. Do you know the command to remove the alternative
> confor
/plueckthun
> http://www.bioc.uzh.ch/plueckthun/antibody
> http://www.bioc.uzh.ch/plueckthun/nanowelt
>
>
>
>
>
>>
>>
>> Message: 6
>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>> From: harold steinberg
>> Subject: [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
/3j5q/C/E/ILE`573/C
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 mainta
This is exactly the kind of question students ask… could you please put this in
the wiki if it’s not already there?
Thanks!
> On Apr 8, 2016, at 2:44 PM, Thomas Holder
> wrote:
>
> Hi Amin,
>
> Multi-line labels are supported in Incentive PyMOL 1.7.0 and later. Simply
> use a linefeed char
ome 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 wrote:
>
>> Hi All,
>>
>> I’m
kthun/antibody
> <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:pymo
t doesn't exist.
>
> Cheers,
> Jared
>
>> On Apr 8, 2016, at 11:42 AM, harold steinberg > <mailto:h.adam.steinb...@gmail.com>> wrote:
>>
>> Sorry to be inept… I've never had the opportunity to learn beyond the basics
>> of Unix.
>>
vid Hall wrote:
>
> Make a file at ~/.pymolrc
>
> -David
>
>> On Apr 8, 2016, at 10:35 AM, harold steinberg
>> wrote:
>>
>> where in OS X is pymolrc located?
>>
>>> On Apr 7, 2016, at 2:39 PM, Thomas Holder
>>> wrote:
>&g
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
--
___
PyMOL
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? (I
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 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 rainbo
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