I think this becomes less of an issue with practice. This problem is exaggerated in blitz where it is vital to simply "see" tactical patterns immediately. In slower time controls its less of an issue. Usually in correspondence or slower time control online games I set up the pieces on a real board and look at that to calculate rather than the screen. Better for my eyes and for my OTB chess.
Playing Chess on devices hurts my ability with physical chess boards
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For me, the trouble initally was having my eyes adjust from 3D OTB to 2D on the PC or phone. I have since adjusted, and I think you will acclimate in due time.
Has this happened to anyone else? So I've started playing chess again after some years break. I can analyze and calculate well on a digital flat surface like ipad or computer, but when I try playing on a real board and pieces I just have difficulty thinking right. Has this happened to people? Is there an easy way to train thinking on board like on digital devices?