[modeller_usage] questions concerning hydrogen in optimization

[abdullah ahmed <>]

Dear Laurent,

I have a question regarding optimization using "cg.optimize". The optimized structures/proteins produced after using this function are always without hydrogens. So does this mean that:

1. The optimization procedure removes hydrogens and does not use them during the optimization steps?
2. If the above is true, is there a way to conduct optimization with hydrogens included? 

Thanks in advance,
Abdullah

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