[PyMOL] Serine phosphorylation

2018-07-31 Thread Wei Song
Hi all, I have a peptide structure and would like to phosphorylate one of the serine residues to test its binding capacity to a ligand. I tried the Build function with a PyMol 2.0, but only a phosphorous can be added to the serine. Does anyone have experiences of creating a phosphorylated residue

Re: [PyMOL] Atoms forming more bonds than they should have

2018-07-10 Thread Wei Song
stance based bonding when > loading data from PDB files. Which docking program generated this file? > > Cheers, > Thomas > > > On Jul 9, 2018, at 4:57 PM, Wei Song wrote: > > > > Hello, > > > > I got a structure (attached figure) of a lipid after d

[PyMOL] Atoms forming more bonds than they should have

2018-07-09 Thread Wei Song
Hello, I got a structure (attached figure) of a lipid after docking it with a protein. The original structure before the docking is in SDF file, not regular PDB. I've never seen a docked structure like this with many of the atoms having more bonds than they actually can have like some carbons