Hello Qinhong--

> 
> I have tried a lot of server and software to do this. However, the naming of
> hydrogen always doesn't fit Xplor-NIH. Is there any way to add hydrogen to
> crystal structure so that it can be used as a starting structure?
> 

Certainly. Just calling 

import regularize
regularize.addUnknownAtoms_new()

after loading psf and coordinates should do the trick.

best regards--
Charles
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