Color files, isosurfaces, overlays

[Melissa Lucero]

1. Is there a way to reset the default colors in Vesta so the changes made for one molecule are permanent, i.e., so when a new cif file is open 2 days later, the color scheme is not the VESTA colors as shipped, but the one set by the user?
2. Is it possible to change the color of ONE isosurface area in a manner analogous to that for atoms? e.g., highlight the electron density on terminal amino groups differently from the rest of molecule, which is in one color.
   
3. Is there a way to overlay 2 structures quickly and perhaps calculate the RMSD?

I will gladly write up how-to's for these and others and send them back to VESTA if these procedures can be done in a reproducible way. I have to do this for my co-workers, now. If it was shared on the webpage, that would be better for everyone. I just do not know how to do these things reproducibly, so it is unwise to call them "how-to's" at this juncture.

[Koichi Momma]

> 1. Is there a way to reset the default colors in Vesta so the changes

> made for one molecule are permanent, i.e., so when a new cif file is
> open 2 days later, the color scheme is not the VESTA colors as
> shipped, but the one set by the user?

Default colors and radii of atoms are stored in a text file named
"elements.ini".
It contains the following data in each column.
atomic number,
atomic symbol,
atomic radius,
van der Waals radius,
ionic radius,
color (R, G, B).


> 2. Is it possible to change the color of ONE isosurface area in a

> manner analogous to that for atoms? e.g., highlight the electron
> density on terminal amino groups differently from the rest of
> molecule, which is in one color.

No. Isosurfaces of the same level are always rendered with a same color.
Only isosurfaces of different levels can have different colors.


> 3. Is there a way to overlay 2 structures quickly and perhaps
> calculate the RMSD?

No, but I agree that such feature is useful. Maybe I should consider
adding such feature in the future.

> I will gladly write up how-to's for these and others and send them
> back to VESTA if these procedures can be done in a reproducible way. I
> have to do this for my co-workers, now. If it was shared on the
> webpage, that would be better for everyone. I just do not know how to
> do these things reproducibly, so it is unwise to call them "how-to's"
> at this juncture.

That would be great!
How-tos are probably the most important "missing feature" of VESTA :)

Best regards,
Koichi


--
Koichi Momma
National Museum of Nature and Science
4-1-1, Amakubo, Tsukuba, Ibaraki 305-0005, Japan
TEL: +81-(0)29-853-8163
FAX: +81-(0)29-853-8998
k-m...@kahaku.go.jp
vest...@gmail.com