RDCvis & KiNG: Difference between revisions
JeremyBlock (talk | contribs) No edit summary |
JeremyBlock (talk | contribs) No edit summary |
||
| Line 5: | Line 5: | ||
Draft Outline | Draft Outline | ||
== | == Intro to RDCvis == | ||
<span>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.</span><!--EndFragment--> | <span>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.</span><!--EndFragment--> | ||
<!--[if gte mso 9]><xml> | <!--[if gte mso 9]><xml> | ||
| Line 113: | Line 113: | ||
mso-bidi-theme-font:minor-bidi;} | mso-bidi-theme-font:minor-bidi;} | ||
</style> | </style> | ||
<![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). | <![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). | ||
<br> | <br> | ||
| Line 120: | Line 120: | ||
<span>RDCvis allows users to visualize and interact | <span>RDCvis allows users to visualize and interact | ||
with the possible RDC curve shapes.<span> </span></span> | with the possible RDC curve shapes.<span> </span></span> | ||
IMAGE <span>These varied curve shapes | IMAGE <span>These varied curve shapes | ||
| Line 127: | Line 127: | ||
internuclear bond vector.<span> </span></span>IMAGE | internuclear bond vector.<span> </span></span>IMAGE | ||
== <br> | == <br>Getting RDCvis to work in KiNG == | ||
=== | === Walk-through of loading RDCs === | ||
==== | ==== What you need - ==== | ||
===== a) MolProbity multimodel-multicrit kinemage ===== | ===== a) MolProbity multimodel-multicrit kinemage ===== | ||
| Line 139: | Line 139: | ||
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. | ||
==== | ==== Loading the files - screenshots ==== | ||
=== | === Co-centering tool === | ||
==== | ==== Wal through of co-centering tool - screenshots ==== | ||
== | == Using RDCvis to analyze RDCs in their local context<br> == | ||
=== | === Analysis with one or multiple RDCs === | ||
==== | ==== Patterns to look for ==== | ||
===== | ===== Orientation Dependent Variability ===== | ||
=== | === Using other helpful data<br> === | ||
==== | ==== Talos+ restraints ==== | ||
==== | ==== Order parameters ==== | ||
==== | ==== Sterics and geometry from MolProbity ==== | ||
== | == Using RDCvis in iterative refinement of NMR structures == | ||
Revision as of 16:02, 1 November 2011
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 -
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.