Hi Fred,
On 14/10/2019 08:46, Fred Vellieux wrote:
>
> I am working on "non-standard" small molecules (docking to protein structures). To generate pdb files I use
> molview.org (for drawing and then generating .mol files, see the attached picture file molecule.jpg)
You can draw and edit mol files in Coot. If I am allowed to bang on my own drum, I'd say that the 2D
representations are rather high quality.
> then
> babel to convert to the pdb format
Convert your mol files to 3D PDB files (or mmCIF) using Acederg, Pyrogen, or Grade.
Pressing "Accept" should run one of those programs - depending on your binary distribution.
>
> Even though the geometry is correctly defined at the stage of molview.org, the "definitions" (of
> connectivities, bond types etc) are all lost during the conversion.
>
> The pdb files give the type of pictures enclosed in coot or pymol (attachments) that aren't suitable for
> publication purposes.
<snicker> - the bond lengths are 1.0 I suppose. Coot uses a default bond length of 1.5 so if you look at the
2D mol file directly it will appear moderately sane.
Paul.
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