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From: Lizelle Lubbe (LBBLIZ002_at_myuct.ac.za)
Date: Fri Mar 16 2018 - 09:31:37 CDT

Hi

I have simulated the behaviour of 2 glycoproteins (homologs) and would like to compare the volume occupied by sugars at each glycan site between the two proteins. This would identify changes in the glycans' dynamic range due to unique protein interactions etc.

I’ve used VMD's Volmap extension to produce and visualize .dx occupancy volmaps and visually observed differences.
Is there any way in which I can calculate exact volume values per glycan in cubic angstroms to quantitatively compare? Haven’t been able to figure out a way to do this.

I would like an output like fig 2 in Yang et al 2017 (doi:10.1038/s41598-017-04532-9) but they don't mention the software used in calculating the volume

Kind regards

Lizelle Lubbe
PhD Chemical Biology
University of Cape Town
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