Hello sir , I have multiple chain protein . In the model loop i can only fix one chain but my protein missing residues in all chains now how to do them all togather . And when i save the modeled file . I can only see the chain which was modeled rest chain get removed in new saved file
Yes, Chimera uses either locally installed Modeller software or web service ( Modeller) for the modeling and refinement of loop region(s). Script first generate an initial model and then several loop conformations are generated based on initial loop conformation. So optimization algorithm is active in this case. You can click on the given link for more details.. salilab.org/modeller/manual/node499.html
@@jeevikasilicobio Does it apply optimization to only modeled part? I want to keep the rest of the protein as it is. So in such a case, can I use Modeller in Chimera or should I write a script for it?
@@ecemgungor6208 You can keep rest of the protein as it is. Just select 1 residue adjacent to the missing regions to move.... You can use the web service, no need to write a script.
Dear sir when your protein has both missing residues in loop region and in intermediate regions which option do you choose for modelling, All missing residues?
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Great tutorial thanks à lot.
Glad you enjoyed it!
thank you
Hello sir ,
I have multiple chain protein . In the model loop i can only fix one chain but my protein missing residues in all chains now how to do them all togather . And when i save the modeled file . I can only see the chain which was modeled rest chain get removed in new saved file
FROM BBAU
I have a quick question. Does model/refine loop option in Chimera do any optimization or refinement?
Yes, Chimera uses either locally installed Modeller software or web service ( Modeller) for the modeling and refinement of loop region(s). Script first generate an initial model and then several loop conformations are generated based on initial loop conformation. So optimization algorithm is active in this case. You can click on the given link for more details..
salilab.org/modeller/manual/node499.html
@@jeevikasilicobio Does it apply optimization to only modeled part? I want to keep the rest of the protein as it is. So in such a case, can I use Modeller in Chimera or should I write a script for it?
@@ecemgungor6208 You can keep rest of the protein as it is. Just select 1 residue adjacent to the missing regions to move.... You can use the web service, no need to write a script.
@@jeevikasilicobio Thank you so much! Please keep recording videos on MD and analysis/modeling! It is very useful for beginners! Thanks!
Dear sir when your protein has both missing residues in loop region and in intermediate regions which option do you choose for modelling, All missing residues?
Yes, in that case, you can use all missing residues options
Hello sir
can u please tell me it is necessary to save all models in a file or is it ok if we save only single model
Sir can you please provide me key