1VJU: TLSMD Thermal Parameter Analysis of Structure

TLS Partitions and Motion Analysis of Individual Chains

For each protein chain, this analysis show the optimal division into 1 TLS group, 2 TLS groups, 3 TLS groups, etc, up to 20 groups. It goes on to analyze the implied rigid body translational and rotational motion of each group, as well as its quality of fit to the refined atomic displacement parameters (B-factors). If you have multiple chains in your structure, they are treated independently. 1VJU: Chain A TLS Analysis 1VJU: Chain B TLS Analysis

When multiple chains are present in your input structure, a side-by-side sequence alignment is generated to show how the TLS group selection for one chain aligns with the selection for the other chains. This analysis is only meaningful when there are multiple chains of the same sequence in the asymmetric unit.

1VJU: Multi-Chain Alignment Analysis of TLS Groups

The CCP4 refinement program Refmac5 and the PHENIX program PHENIX.refine both implement a refinement mode in which individual isotropic temperature factors are supplemented by refinement of one or more TLS groups. TLSMD will help you choose how many TLS groups to subdivide your protein chains into, and it will generate a input files for you to use in further refinement using Refmac5 or PHENIX.

1VJU: Generate input files for multigroup TLS Refinement