<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear colleagues,</div><div><br></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;">Regarding H addition to protein structures, there are indications that hydrogens of NH3+ groups of lysine or N-termini, and side chain methyls of methionines need a rotational optimization (Richardson & Richardson, Chapter 15 in "Structural Bioinformatics", 2nd ed., 2009, p. 380) . I think this problem is not too common, but I did encounter it at least once when
I had to rotate manually a Methionine methyl to remove a clash with
the ligand. I think Chimera doesn't perform this optimization, or does it? If it doesn't, perhaps this could be put on a list of future improvements:)</div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;">Best regards,<br></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;">Vis Kairys<br></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;">Institute of Biotechnology</div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif;
background-color: transparent; font-style: normal;">Vilnius University<br></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: times new roman,new york,times,serif; background-color: transparent; font-style: normal;"><br></div><div style="visibility: hidden;" title="1348817521999" id="_booktextmark_tab_id_"></div><div style="visibility: hidden;" title="1348817522194" id="_booktextmark_tab_id_"></div></div></body></html>