Hi there,
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)
then babel to convert to the pdb format.
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. Hence I am
wondering if there is a simple pdb editor that allows to define the
geometry, bond type, write CONNECT cards etc in order to generate
"proper" pdb files. Or any other way to do this without having to
understand these very special PDB cards and trying to do it manually.
Sorry about including image files but the total size is less than 150 kb.
Thanks in advance for advice.
Fred.
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
|