RE: How many models to generate?
Hello Charlotte Habegger-Polomat,
I am not an expert modeller user, but what I can "share" about it? I think the number of models generated depends on available time and computational power you have to carry it. I usually generate between 100 and 200, and select that model with the lowest "current energy". Probably somebody could discuss it better, anyway, I tried ;)
Frederico Arnoldi UNESP - Rio Claro - Brazil
> >Dear Modeller users, > >I was wondering if others would share how many structures you usually >generate for a family of models. > >I am currently working on modelling my protein of interest with 3 known >template structures (>30% sequence similarity). When using Modeller, I >generate a family of 20 models and then evaluate the variability and >quality of models within the family. > >How many do other Modeller users generate? > >How do you decide on this number? > >I've read articles where 3 models, others where 30 models were generated >with Modeller... > >Thanks! > >-Charlotte Habegger-Polomat
Hello Frederico Arnoldi!
Thanks for your answer...I have been generating 20 models for my protein of interest, and after evaluating the variability within the family of models, I select one or more models to work with.
This reminds me that I have only an "approximation" of my structure, and also allows me to retain some variability. I then work with these models as one would work with a family of NMR structures.
Does anyone else use more than one model to work with after generating a family with Modeller?
Thank you!
-Charlotte Habegger-Polomat
Frederico Arnoldi wrote:
> Hello Charlotte Habegger-Polomat, > > I am not an expert modeller user, but what I can "share" about it? > I think the number of models generated depends on available time and > computational power you have to carry it. I usually generate between > 100 and 200, and select that model with the lowest "current energy". > Probably somebody could discuss it better, anyway, I tried ;) > > Frederico Arnoldi > UNESP - Rio Claro - Brazil > >
participants (2)
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Charlotte Habegger-Polomat -
Frederico Arnoldi