Question: Spherical coordinates of 3D structure of gene
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gravatar for kingkenshin1997
2.1 years ago by
kingkenshin19970 wrote:

Does anyone have any code to get the spherical coordinates of the 3D structure of gene(3D structure is in .pdb format)?

gene • 528 views
ADD COMMENTlink modified 2.1 years ago by Alex Reynolds31k • written 2.1 years ago by kingkenshin19970
1

Please don't post similar questions multiple times. You had already received an answer from @Alex to last question : Equirectangular projection of 3D structure of gene

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by GenoMax95k

a "gene" ? you meant a protein, a RNA, or a DNA ?...

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum133k

How about https://www.ncbi.nlm.nih.gov/pubmed/21956738 ?

Not sure what advantage there is to using spherical coordinates over cartesian though...

ADD REPLYlink written 2.1 years ago by Joe18k
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gravatar for Alex Reynolds
2.1 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

Perhaps use PyMOL to export Cartesian coordinates from a PDB file or selection within a PDB: https://pymolwiki.org/index.php/Get_Coordinates_I

Maybe this paper will help point you to code to turn Cartesian coordinates into spherical coordinates: https://arxiv.org/abs/1512.00424

In this 2011 paper (Reyes, V.M., 2011), we reported on our efforts at representing spheroprotiens using spherical (ρ, ϕ, θ) coordinates, with the protein centroid as origin, and presented two of its potential applications. Here, we present the Fortran program source codes we used in our procedure, starting with the determination of the protein molecular (geometric) centroid and the transformation of its Cartesian coordinates to spherical coordinates. We also present here the Fortran source codes for the implementation of the two applications we presented in the aforementioned paper, namely, the separation of the protein outer layer (OL) from its iner core (IC), and the identification of protrusions and invaginations on the protein surface.

Once you have rho, phi and theta in some matrix text file, you could perhaps import that into R and use ggplot and its stat_density_2d function to plot phi and theta along x and y axes, and use rho as the heatmap "density" value.

Lots of examples online on how to make that type of plot with sample datasets, which you'd adjust for your particular coordinates.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Alex Reynolds31k
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