Entering edit mode
10.1 years ago
willemveerman
•
0
I am trying to draw a protein structure from a pdb file using pymol.
However, when I try to run the script below, a pymol window opens but it is just pitch black. Also, bizarrely, the pdb file is outputted to the shell.
Here is my code:
bioservices_pdb_obj = PDB()
pdb_file = bioservices_pdb_obj.getFile(results[str(Brick.part_attrib(self,'uniprot_id'))][detail-1],'pdb')
pdb_name = str(Brick.part_attrib(self,'uniprot_id'))
pymol.finish_launching()
pymol.cmd.load(pdb_file, pdb_name)
pymol.cmd.disable("all")
pymol.cmd.enable(pdb_name)
pymol.cmd.png("my_pdb.png")
pymol.cmd.quit()
Does anyone know what is going on here?
The .png file 'my_pdb' is dumped into the working directory, but that's just black as well.
That does not look like native pymol code. Where does the PDB() object come from? You do know that pymol has a built-in command for fetching files from PDB, right?