Hi Pedro,
Try these two changes:
# shape - 1
xinc, yinc, zinc = (
abs(xmax - xmin) / (field.shape[0] - 1),
abs(ymax - ymin) / (field.shape[1] - 1),
abs(zmax - zmin) / (field.shape[2] - 1),
)
# position rounding by +0.5
idx = (
int((at.coord[0] - xmin) / xinc + 0.5),
int((at.coord[1] - ymin) / yinc + 0.5),
int((at.coord[2] - zmin) / zinc + 0.5),
)
Cheers,
Thomas
> On Nov 8, 2020, at 11:20 AM, Pedro Lacerda <pslace...@gmail.com> wrote:
>
> Hi,
>
> I'm using `cmd.get_volume_field(copy=0)` to edit maps. Each grid cell must
> increase by 1 each time the condition `atom.text_type in atomtypes` is met.
>
> But something went wrong and the map mesh didn't align with the atoms.
>
> `ensemble.selection` and `obj` spawns atoms in the exact same positions.
>
>
>
> map_obj = prefix + "." + title
> pm.map_new(map_obj, type="vdw", selection=ensemble.selection)
> field = pm.get_volume_field(map_obj, copy=0)
> if -1 is field:
> colorprinting.error("Unable to get volume field.")
> continue
> xinc, yinc, zinc = (
> abs(xmax - xmin) / field.shape[0],
> abs(ymax - ymin) / field.shape[1],
> abs(zmax - zmin) / field.shape[2],
> )
> field[:] = 0
> for at in pm.get_model(obj).atom:
> if at.text_type in atomtypes:
> idx = (
> int((at.coord[0] - xmin) / xinc)-1,
> int((at.coord[1] - ymin) / yinc)-1,
> int((at.coord[2] - zmin) / zinc)-1,
> )
> field[idx] += 1
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> _______________________________________________
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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