modeller_usage

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modeller_usage@salilab.org

August 2019

3 participants
2 discussions

Modeling missing residues from a second template file
by Danilo Boskovic 20 Aug '19

20 Aug '19

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

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loop modeling
by Rui Chen 20 Aug '19

20 Aug '19

Hello, I am using Chimera (Modeller) to model a loop, which locates at the C-termini of the original crystal structure. The structure of the target protein is a homodimer, however, I cannot model the two chains together. How can I model the two chains together? I modeled chain A and chain B separately, the loops I modeled have different configurations. Could you please help me resolve the problem? Best regards, Rui

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