Radius of gyration
Radius of gyration is specified with two flags:
Flag "-rgyr_res" is used to specify the first and the last residues of a protein region that should be included in calculations of radius of gyration. A good strategy is to exclude N- and C-termini with S2 < 0.7 (as reported by the RCI webserver www.randomcoilindex.com ).
Flag "-rgyr_value" is used to specify radius of gyration for these residues under an assumption of a globular structure (see equation at http://nmr.cit.nih.gov/xplor-nih/xplorMan/node412.html )
Only radius of gyration for monomeric proteins is currently accepted. See an example of arguments for radius of gyration of ubiquitin below.
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-rgyr_value 11 -rgyr_res 2:72
where 2 and 72 are the first and the last residues, respectively, of ubiquitin region to be included in calculations of radius of gyration
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Problems? Suggestions? Please
contact Wishart group
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