App created by Dr. Jared-Adolf-Bryfogle (; , in collaboration with Dr. Sebastian Raemisch ( and Dr. Jason W. Labonte (;

PIs: Lab of Dr. William Schief ( and Dr. Jeff Gray (


Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design Jared Adolf-Bryfogle, J. W Labonte, J. C Kraft, M. Shapavolov, S. Raemisch, T. Lutteke, F. Dimaio, C. D Bahl, J. Pallesen, N. P King, J. J Gray, D. W Kulp, W. R Schief bioRxiv 2021.09.27.462000;


A pilot app specifically for glycan clashes which quantifies clashes between specified glycan branches and other chains and glycan branch - glycan branch clashes. Does not count clashes for intra glycan branch. Does not echo input files, adds info to output scorefile to allow for MPI runs.

Clash Definition

Atom is clashing if it clashes with ANY other atom Count up clashes (hard and soft) per-residue

  • Hard:
    • distance <= LJ1 + LJ2
  • Soft:
    • distance <= (LJ1 + LJ2) * (1 - S). S is between 0 and 1. Here, we use .33 as default.

-> Intuitive definition, easily conceptualized, still quantitative

Relevant Options:

-glycan_branches, vector
 - Required. Vector of glycan branches.  
 - Rosetta Residue numbering or PDB like RosettaScripts

-chech_chains, vector
 - Required. A list of [glycan or protein] chains to compute chain-based clashes.  
 - If not given, will only compute glycan-glycan clashes!

-ignore_hydrogens, boolean
 - Should we calculate only heavy-heavy atom clashes?

-soft_clash, Real
  - When we calculate atom-atom distances using LJ distances, 
  - clash if distance < (atomI_LJ + atomJ_LJ)*(1 - soft_clash)

See Also

RosettaScript Components