Re: [PyMOL] Map to cartoon

[Jarrett J. <jar...@sc...>]

Hi Mark,

Great question. I currently cannot see a way to do so. I think the color
command when providing a ramp should, by intention, color the cartoon, but
there may be a bug or this might not have been implemented yet (the cartoon
removes its color and is set to white). I have a workaround if the only
thing you need to do is color atoms by proximity to another object (using
the example from the `ramp_new` PyMOLWiki documentation). Note that the
color smoothing is not as good as using the `ramp_new` command:

from pymol import cmd

def set_property_proximity_to(obj, target, ramp='red yellow', minimum=None,
maximum=None):
    ligand_atoms = []
    cmd.iterate_state(0, target, 'ligand_atoms.append((x, y, z))', space=
locals())

    def find_nearest_dist(x, y, z):
        min2 = min((x - x1) ** 2 + (y - y1) ** 2 + (z - z1) ** 2
                   for x1, y1, z1 in ligand_atoms)
        return min2 ** 0.5

    nearest_ds = []
    cmd.alter_state(0, obj, 'nearest_ds.append(find_nearest_dist(x, y, z))',
space=locals())

    # Hijack 'b' property for closest distance
    cmd.alter(obj, 'b = nearest_ds[index-1]', space=locals())
    cmd.spectrum('b', palette='red yellow', selection=obj, minimum=minimum,
maximum=maximum)


cmd.fetch('1rx1')
cmd.extract('ligand', 'organic')
set_property_proximity_to('1rx1', 'ligand', ramp='red yellow', minimum=4,
maximum=8)
cmd.color('blue', 'ligand')
cmd.show('surface', 'ligand')

I'll do some investigation regarding why ramp coloring for cartoons isn't
working as intended (assuming there isn't something I'm missing already).

Hope this helps,

Jarrett J

On Mon, Jul 24, 2023 at 1:27 PM Foster, Mark <fos...@os...> wrote:

> Thanks Jarrett for the response.
>
>
>
> I think `spectrum` should work, but I can’t figure out how to access the
> proximity parameter calculated by `ramp_new` in order to use it directly
> (e.g., “p.prox”), or to map it to the b factor.
>
>
>
> Does ramp_new store the values in an array?
>
>
>
> -M
>
>
>
>
>
> *From: *Jarrett Johnson <jar...@sc...>
> *Date: *Monday, July 24, 2023 at 12:02 PM
> *To: *Foster, Mark <fos...@os...>
> *Cc: *pym...@li... <pym...@li...
> >
> *Subject: *Re: [PyMOL] Map to cartoon
>
> Hi Mark, Does the `spectrum` command cover your use case? https:
> //pymolwiki. org/index. php/Spectrum . You can specify an atomic property
> and map specified colors to a range of the given property. Hope that helps,
> Jarrett J. On Mon, Jul 24, 2023
>
> Hi Mark,
>
> Does the `spectrum` command cover your use case?
> https://pymolwiki.org/index.php/Spectrum
> <https://urldefense.com/v3/__https:/pymolwiki.org/index.php/Spectrum__;!!KGKeukY!2YCpuhVe5GRqx_4jegX3LkI02R8BJqaQz4vDGwiaUTk4P0DKAA-uma5ffkB7b706ohBs7I5Alp7QFqei3X8edZnW_j-ow-ipqQ$>
> . You can specify an atomic property and map specified colors to a range of
> the given property.
>
> Hope that helps,
> Jarrett J.
>
>
>
> On Mon, Jul 24, 2023 at 9:21 AM Foster, Mark <fos...@os...> wrote:
>
> PyMOL fans,
>
>
>
> Is possible to use ramp_new to color cartoons, in addition to atoms and
> surfaces?
>
>
>
> I assume ramp_new stores the property to be mapped in a variable that
> could be used for the CA atom color.
>
>
>
> color prox, (sele) sets the color of each atom, but not the cartoon.
>
>
>
> Thanks in advance,
>
>
>
> -M
>
>
>
>
>
> —
>
> Mark P. Foster, Professor, he/him
> Department of Chemistry and Biochemistry
> The Ohio State University
> 734 Riffe Building
> 484 West 12th Ave.
> Columbus, OH 43210-1214
> (614) 292-1377
> fos...@os...
> http://go.osu.edu/fosterlab
>
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> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
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-- 

*Jarrett Johnson* | Senior Developer, PyMOL