It's usually difficult to say what the problem is without the merged.pdb file.  But if the dssp command fixes things, then it there's probably an error in the secondary structure information in the merged.pdb file, or lack thereof.   If you remove all of the HELIX and SHEET records from merged.pdb, then ChimeraX will compute the secondary structure needed for the cartoon display. Alternatively you could use a DSSP web server, like http://www.cmbi.umcn.nl/xssp/ or https://pdb-redo.eu/dssp (there are probably others), to generate the complete HELIX and SHEET records and put those in your merged.pdb file.    HTH,    Greg On 10/7/2025 8:06 PM, Rayees Mattoo via ChimeraX-users wrote:

Hi, I merged two molecules in coot and generated a merged.pdb file. However, upon displaying in ChimeraX part of my model is cartoon and part of it displays as worm, see the attachment. After running dssp I can fix it, but I want it to display as cartoon by default. Anything I need to edit in the merged.pdb file?

Best Rayees

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