Actually, I generated 5 models by using modeller and done side chain repacking on it by RASP (RApid Side-chain Predictor). Now, I want to validate side chain repacked models by comparing DOPE score between before and after side chain repacking but I don’t have any idea about the external tools which calculate DOPE score alone or separate script in modeller. So If some one knows any tool or how to do it with modeller would be nice to calculate DOPE SCORE for side chain repack models.
Thanking you in advance
Dear all ,
I found out the following script in modeller itself which can calculate the DOPE SCORE alone.
# Example for: selection.assess_dope()
from modeller import *
from modeller.scripts import complete_pdb
env = environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
# Read a model previously generated by Modeller's automodel class
mdl = complete_pdb(env, '../atom_files/1fdx.B99990001.pdb')
# Select all atoms in the first chain
atmsel = selection(mdl.chains[0])
score = atmsel.assess_dope()
- Badges
- Science topic
- Similar topics
- Chemistry
- Biochemistry