Warren.
I can't speak to the alignment tools, as I don't spend a lot of time in
homology model building, but I would like to second the idea of adding the
selection keywords. They would make my use of pymol that much easier.
Andy
--On Wednesday, May 19, 2004 09:32:17 -0700 Warren DeLano
<war...@delanoscientific.com> wrote:
Thanks for the input.
* sequence colors could (optionally?) match atom (C-alpha)
colors in the 3D view.
Good idea.
* When a 3D-alignment is done, there is a sequence alignment behind.
Having this transferred to the sequence window would be
extremely useful.
Planned -- but this is nontrivial.
* The heteroatoms should not appear in the sequence windows
- at least not in "residue" modes.
Hmm. Some heteroatoms you definitely want, like S-met and modified bases.
Others like water aren't quite so useful.
What we may need in PyMOL is a set of categories/selection keywords such
as the following:
"polymers": all natural bases/amino acids and any hetatms connected
through main chain chemistry
"waters": all recognized waters (HOH, WAT, TIP, etc.)
"ions": isolated atomic cations, anions, metals, etc.
"ligands": anything not contains in the above
By default, polymers and ligands make sense in the sequence view and
waters can probably be omitted. Ions we should also probably keep in by
default since they often play important roles in coordinating ligands.
Does this sound like a useful addition?
Cheers,
Warren
