Modeling missing residues from a second template file
Dear Ben,
Is it possible? I know that i can model residues according to the tutorial: select the residues and use as a template to model the full structure. So i did it and the structure was severely impacted (RMSD 0.25). Loopmodel de-novo can do it without problems although i wish i could utilize my other structure file that is basically just a different conformation due to a ligand, but the deviation at the positions where the residues are missing are minuscule.
If not then i have two choices: de-novo and the automodel with a change in conformation of 0.25 RMSD. Which one would you choose?
Sincerely,
D. Boskovic
Dear Ben,
Worth noting: i will use the output file to model something else.
D. B.
On Thu, 15 Aug 2019 at 17:25, Danilo Boskovic daniloboskovic0095@gmail.com wrote:
> Dear Ben, > > Is it possible? I know that i can model residues according to the > tutorial: select the residues and use as a template to model the full > structure. So i did it and the structure was severely impacted (RMSD 0.25). > Loopmodel de-novo can do it without problems although i wish i could > utilize my other structure file that is basically just a different > conformation due to a ligand, but the deviation at the positions where the > residues are missing are minuscule. > > If not then i have two choices: de-novo and the automodel with a change in > conformation of 0.25 RMSD. Which one would you choose? > > Sincerely, > > D. Boskovic >
On 8/15/19 8:25 AM, Danilo Boskovic wrote: > Is it possible? I know that i can model residues according to the > tutorial: select the residues and use as a template to model the full > structure. So i did it and the structure was severely impacted (RMSD > 0.25).
If you really want to do this, note that Modeller by default will try to move all atoms to best satisfy the restraints. If you want the non-missing residues to be exactly the same as the input, make sure you only select the missing residues for refinement in select_atoms(), as per https://salilab.org/modeller/9.22/manual/node23.html
Ben Webb, Modeller Caretaker
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Danilo Boskovic -
Modeller Caretaker