PDB: 1HIG, when opened using Accelrys DS Visualizer, Avogadro and Jmol produces a series of dots in space and cannot be displayed as 3D ball and stick models. Is there any way to overcome this problem?

This is the output from Accelrys DS Visualizer 4.0: This is the output from Accelrys DS Visualizer 4.0

This is the output of Avogadro:

enter image description here

This is the output of Jmol: This is the output of Jmol


1 Answer 1


This specific PDB file only contains the coordinates of all the $\ce{C_{\alpha}}$ atoms of the protein. It simply does not contain enough information to display an actual 3D structure of the protein.

The file does contain secondary structure assignments, so it should probably be possible to create a cartoon display of the protein, but that would require more than a simple PDB viewing program. But there is no way to create a ball-and-stick model with the data contained in that file.

  • $\begingroup$ There is a mmcif file in the archive, but I am unable to open it with mercury or any other molecular viewer I have installed. $\endgroup$ Dec 9, 2014 at 12:09
  • $\begingroup$ To add to the answer above, the pdb file only contains Ca atoms and as such it is not possible. However the structure 1EKU should be usable instead. $\endgroup$ Apr 13, 2017 at 23:15

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