>P1;original1.1.24351.test
sequence:original1.1.24351.test:1 : :21 : :::-1.00:-1.00
DVAVKILKVVDPTPEQFQAFR*
>P1;4G0N
structure:4G0N: :B : :B :::-1.00:-1.00
DCLMKALKVRGLQPECCAVFR*
I do get the model from this pir alignment file. However, does not mentioning the "start" and "end" residue of the PDB file influence the quality of the structure? or influence the model any way?
Am I right, if I say, that modeller by default takes the residues of chain "B", finds the corresponding residues in chain B and correctly models the sequence as per the alignment.
Please let me know of your comments.
Thanks much!
PS:AjasjaBest,Hi David!Dope is used to measures the quality of the model. (How PDB-like are some distributions).
Your last line should probably be:
s0s1.energy() - (s0.energy() + s1.energy())You can write '%s:A'%str(2) more elegantly as '%d:A'%2On 28 October 2016 at 12:31, David De Sancho <" target="_blank">> wrote:______________________________Dear BenThanks for the quick response. However I find something really puzzling for a few tests. Mainly, that interface energy turns out to be unfavourable.In the link below I include a gist with a self explanatory example of how this turns out to be. It corresponds to the interface between two helices in the designed a3D protein but I’ve tried with others too.Surely there is something about my selections that’s not right, but any hints at what’s going on would be very helpful.Thanks,DavidOn 26 Oct 2016, at 22:00, Modeller Caretaker <" target="_blank">> wrote:On 10/26/2016 08:41 AM, David De Sancho wrote:I’m handling a problem where it is important to evaluate energies of
interfacial residues (e.g. interface residues between two helices in a
protein). In order to carry out this energy evaluation with Modeller, I
start by producing a model for the protein. Then I generate two
selections (e.g. one for each helix). Would it be possible to calculate
the energy for residues in the interface between both selections?
Calculating the energy of only the interactions between selections s1 and s2 isn't possible to do directly in Modeller, but there's a simple workaround: calculate the energy of the union s1+s2, then subtract the two energies of s1 and s2 by themselves. You'll probably also want to set nonbonded_sel_atoms to 2:
https://salilab.org/modeller/9.17/manual/node140.html
Ben Webb, Modeller Caretaker
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