[phenixbb] secondary structure presentation in VMD

CPMAS Chen cpmasmit at gmail.com
Sun Jan 21 07:04:05 PST 2018

Hi, Phenix users,

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

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?


Best Regards,




Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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