I have docked my protein with a ligand. When I am checking the polar and non polar contacts, I am getting the residues different in Pymol and LigPlot. Can someone please help me with this.
Hi Pratyasha Bhowal ,
In general, each software calculates the distance differently.
I'm not sure about PyMol but you can change the preference in LigPlot.
As long as you have the specifics from PyMol, input them in the LigPlot's preferences and you should get similar results.
Hope this help all the best.
Pratyasha Bhowal
Hi hope you will doing good
Each software works on a different algorithm. Maybe you haven't specified the ligand in the active site using Pymol because in Pymol 10 conformation of ligand present but in Ligplot which one you have opened it's not confirm so first of all specified the ligand conformer that you want to visualize.
Note that the output of the liplot is 2d, since the pymol is 3d...
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