Hi,
Is there any Denovo loop remodeling on the base of the fragment data base in MODELLER?
Cheers, Berk
On 6/28/13 7:56 AM, Ramin Ekhteiari wrote: > Is there any Denovo loop remodeling on the base of the fragment data > base in MODELLER?
Modeller uses a statistical potential for de novo loop modeling, not a fragment database.
Ben Webb, Modeller Caretaker
Is there any rmsd-energy.py script in modeller to calculate the RMSD and energy of all generatedpdb files with template. Data Plot: Energy vs Rmsd?
Thanks Cheers,
________________________________ From: Modeller Caretaker modeller-care@salilab.org To: Ramin Ekhteiari ramin_ekh@yahoo.com Cc: "modeller_usage@salilab.org" modeller_usage@salilab.org Sent: Friday, June 28, 2013 6:15 PM Subject: Re: [modeller_usage] Denovo loop remodeling
On 6/28/13 7:56 AM, Ramin Ekhteiari wrote: > Is there any Denovo loop remodeling on the base of the fragment data > base in MODELLER?
Modeller uses a statistical potential for denovo loop modeling, not a fragment database.
Ben Webb, Modeller Caretaker
On 06/28/2013 08:43 AM, Ramin Ekhteiari wrote: > Is there any rmsd-energy.py script in modeller to calculate the RMSD and > energy of all generated pdb files with template.
You can use selection.superpose() to get the RMSD, but RMSD between target and template is essentially meaningless (a better comparison for benchmarking would be against the native structure of the target sequence). loopmodel already gives you the energies (they're also in the generated PDB files).
Ben Webb, Modeller Caretaker
participants (2)
-
Modeller Caretaker -
Ramin Ekhteiari