RDCvis & KiNG

 This page is under construction as of November 1st, 2011.  

Draft Outline

Intro to RDCvis

Visualizing the RDC curves in their structural context, especially when combined with other structure quality visualizations allows users to easily identify and study areas of their models which need improvement.

Software for generating RDC visualizations, dubbed RDCvis and built into KiNG (Chen, 2009), requires a PDB format coordinate file and an NMR restraints file (in CNS format) with RDC data.  RDCvis outputs the RDC visualizations in kinemage format (Richardson, 1992), as a standalone file that is routinely appended onto an existing multi-model kinemage for viewing in KiNG. These curves plotted using the kinemage graphics format, take advantage of the powerful and extensive infrastructure that already exists for manipulating and viewing kinemages in Mage, KiNG, and KinImmerse (Richardson, 1992; Chen, 2009; Block, 2009).

RDCvis draws RDC curves by using singular value decomposition (SVD) (losonczi1999) to calculate a Saupe alignment matrix (saupe1968) from the RDCs.  The method is described in more detail in the Supporting Information.

RDCvis allows users to visualize and interact with the possible RDC curve shapes. 

IMAGE These varied curve shapes arise from the intersection of the surface representing the possible solutions for the RDC equation with the sphere representing the possible positions for a given internuclear bond vector.  IMAGE

Getting RDCvis to work in KiNG

Walk-through of loading RDCs

What you need -

b) .tbl file (note on acceptible formats

One note is that a significant barrier to using RDCvis is the lack of consistency in the deposited NMR restraints files.  A more strictly defined standard data-file format would make RDCvis more straightforward to use and thus routinely useful to a wider community.