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.
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
