Hi,
Please clarify this doubt regarding modeller.
Let say, I have this PIR alignment:
>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!
On Fri, Oct 28, 2016 at 3:04 PM, Ajasja Ljubetič ajasja.ljubetic@gmail.com wrote:
> 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()) > > Best, > Ajasja > > PS: > You can write '%s:A'%str(2) more elegantly as '%d:A'%2 > > > On 28 October 2016 at 12:31, David De Sancho d.desancho@nanogune.eu > wrote: > >> Dear Ben >> Thanks 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. >> https://gist.github.com/daviddesancho/c854203311ec431d0c17fcfff5055e8c >> Surely there is something about my selections that’s not right, but any >> hints at what’s going on would be very helpful. >> Thanks, >> >> David >> >> >> On 26 Oct 2016, at 22:00, Modeller Caretaker modeller-care@salilab.org >> 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 >> -- >> modeller-care@salilab.org https://salilab.org/modeller/ >> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >> >> >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >> > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >