When I load my model the shoulders look a bit wrong, please see attached image. Is there some way to change this and drop down the shoulders? See the steep angle of the clavicle
I have tried to change the marker placement of the CLAV but without any success
You mention that your models looks wrong when you load it, have you tried running your simulation?
It is first when the simulations are performed that all positions, joints etc. are resolved.
The stature you see upon load is only an arbitrary initial positioning of the model (it should however be as good as possible to make it easy for the solvers to position everything afterwards)
I see you are using the MoCap model and it is important that you perform the ParameterIdentification analysis to scale the model correctly.
We have tried both RunParameterIdentification and then RunAnalysis but the shoulders looks like the picture. Could it be something with the marker on the clavicles that is wrong?
You are probably right that is related to the marker protocol.
It is very hard to see for me on the picture, but I would focus on the markers attached to the thorax and pelvis segments to see if the model defined positions correspond with the positions from your experiments. Here is some guidance on how to adjust the markers.