This may be a little off-topic. I have posted this in VMD users mail list. I want to try here too to see if anyone experienced similar issue.

VMD and pymol gave different presentation on the secondary structure of a protein.

During phenix.refinement, I added secondary structure restraints and correctly labelled all helices and sheets. However, VMD does not correctly present the secondary structure in cartoon/new-cartoon presentation.

A little more detail.

In VMD-1.9.4a12, after I loaded the pdb, I chose new cartoon to present the secondary structure. All chains are presented as random coil, the same as tube representation. However, pymol correctly shows the secondary structure of the same pdb file in cartoon representation.

Has anyone encountered similar situation? what would be the fix?

Thanks!