RDCvis & KiNG: Difference between revisions
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1. Intro to RDCvis | 1. Intro to RDCvis | ||
<span | <span>Visualizing | ||
the RDC curves in their structural context, especially when combined with other | the RDC curves in their structural context, especially when combined with other | ||
structure quality visualizations allows users to easily identify and study | structure quality visualizations allows users to easily identify and study | ||
areas of their models which need improvement.</span><!--EndFragment--> | areas of their models which need improvement.</span><!--EndFragment--> | ||
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<![endif]--> <!--StartFragment--> | <![endif]--><!--StartFragment-->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.<span> </span>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). | ||
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.<span> </span>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). | |||
< | <br> | ||
RDCvis draws RDC curves by using singular value decomposition (SVD) | RDCvis draws RDC curves by using singular value decomposition (SVD) (losonczi1999) to calculate a Saupe alignment matrix (saupe1968) from the RDCs.<span> </span>The method is described in more detail in the Supporting Information. | ||
<span>RDCvis allows users to visualize and interact | |||
<span | |||
with the possible RDC curve shapes.<span> | with the possible RDC curve shapes.<span> | ||
</span>Examples of these are shown </span> | </span>Examples of these are shown </span> | ||
IMAGE.... RDCvis_spheres | |||
<br> | |||
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<![endif]--> <!--StartFragment--><span | <![endif]--> <!--StartFragment--><span>These varied curve shapes | ||
arise from the intersection of the surface representing the possible solutions | 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 | for the RDC equation with the sphere representing the possible positions for a given | ||
internuclear bond vector.<span> </span>Examples showing this intersection are shown</span> | internuclear bond vector.<span> </span>Examples showing this intersection are shown</span> | ||
IMAGE... RDCvis_spheres_dots | |||
<span> </span><!--EndFragment--> | |||
2. Getting RDCvis to work in KiNG | <br> 2. Getting RDCvis to work in KiNG | ||
2.1 Walk-through of loading RDCs | 2.1 Walk-through of loading RDCs | ||
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b) .tbl file (note on acceptible formats | 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.<span> </span>A more strictly defined standard data-file format would make RDCvis more straightforward to use and thus routinely useful to a wider community. | One note is that a significant barrier to using RDCvis is the lack of consistency in the deposited NMR restraints files.<span> </span>A more strictly defined standard data-file format would make RDCvis more straightforward to use and thus routinely useful to a wider community. | ||
2.1.2 Loading the files - screenshots | 2.1.2 Loading the files - screenshots | ||
Revision as of 15:51, 1 November 2011
This page is under construction as of November 1st, 2011.
Draft Outline
1. 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. Examples of these are shown
IMAGE.... RDCvis_spheres
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. Examples showing this intersection are shown
IMAGE... RDCvis_spheres_dots
2. Getting RDCvis to work in KiNG
2.1 Walk-through of loading RDCs
2.1.1 What you need -
a) MolProbity multimodel-multicrit kinemage
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.
2.1.2 Loading the files - screenshots
2.2 Co-centering tool
2.2.1 Wal through of co-centering tool - screenshots
3. Using RDCvis to analyze RDCs in their local context
3.1 Analysis with one or multiple RDCs
3.1.1 Patterns to look for
3.1.1.1 Orientation Dependent Variability
3.2. Using other helpful data
3.2.1 Talos+ restraints
3.3.2 Order parameters
3.2.3 Sterics and geometry from MolProbity
4. Using RDCvis in iterative refinement of NMR structures