Hi,

I am following this toturial https://salilab.org/modeller/tutorial/basic.html would you please tell me which script I have to change ?

I want to get the DOPE for both template and the optimised structure

Bests Mohammad

On Mon, Jul 23, 2018 at 8:26 PM Modeller Caretaker < modeller-care@salilab.org> wrote:

> On 7/20/18 1:44 PM, Mohammad Goodarzi wrote: > > 1- I want to plot the DOPE energy plot between the template and the > > model but after running the evaluate_model.py , I only have one > > TvLDH.profile. So how can I get the other profile to be able to plot > > this figure? > > Change the name of the input PDB file and the output profile by simple > editing of the Python script. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >

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 < modeller-care@salilab.org> 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 > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >