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Re: [modeller_usage] DOPE energy plot



Thanks but when I do 

mdl = complete_pdb(env, 'TvLDH.B99990002.pdb')
to 
mdl = complete_pdb(env, 'TvLDH.pdb')

The first one is the one with the lowest energy in my case and the second one is the template. I get exactly the same data from  TvLDH.profile
Is that logical ? how can I evaluate more my models ? 

Thanks a lot 
Mohammad 


from modeller import *
from modeller.scripts import complete_pdb

log.verbose()    # request verbose output
env = environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology
env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters

# read model file
mdl = complete_pdb(env, 'TvLDH.B99990002.pdb')

# Assess with DOPE:
s = selection(mdl)   # all atom selection
s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='TvLDH.profile',
              normalize_profile=True, smoothing_window=15)

On Tue, Jul 24, 2018 at 2:00 PM Modeller Caretaker <">> wrote:
On 07/24/2018 07:42 AM, Mohammad Goodarzi wrote:
> I am following this toturial
> https://salilab.org/modeller/tutorial/basic.html
> would you please tell me which script I have to change ?

That would be the script you mentioned in your original email,
evaluate_model.py.

        Ben Webb, Modeller Caretaker
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