I saw the talaris2013.wts have mentioned that "the 05.2009 ideal coordinates for # the amino acids". May I ask what is 05.2009 ideal coordinates? Where can I find the document for this coordinates standard？ Thanks
It was found that the previously default ideal coordinates (bond lengths and angles) weren't the best for recapitulating structures. So there was some effort expended to refine them slightly.
To the extent that these changes are documented in the peer reviewed literature, it would likely be in Song et al. "Structure-guided forcefield optimization." http://www.ncbi.nlm.nih.gov/pubmed/21488100 or possibly with Tyka et al. "Alternate states of proteins revealed by detailed energy landscape mapping." http://www.ncbi.nlm.nih.gov/pubmed/21073878
Does this mean that `fa_standard_05.2009_icoor` are prefered to the standard `fa_standard`? Will the changes in 05.2009_icoor be merged back into the fa_standard?
They already have been. The changes made with fa_standard_05.2009_icoor coordinates have been incorporated into fa_standard with the weekly releases, and the old "fa_standard" has been renamed to "fa_standard_pre_talaris2013".