VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Jul 09 2018 - 09:35:32 CDT

Repeated segnames or resid/segname combinations. Behind the scenes, merge structures is using psfgen. So if you have repeated segname/resid combinations, only the last one will have coordinates assigned.

-Josh

On 2018-07-06 16:38:31-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

When I try to merge my protein/membrane/ion pdb with my ligand pdb using the merge structures plugin, the merged pdb has the correct coordinates for the ligand, but the coordinates for the protein, membrane, and ions has all zeroes in their columns. I don't get any errors during the merge process, it just seems to erase the coordinates except for the ligand. What might be causing this? Thanks!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602