Closed russell-taylor closed 1 year ago
russell-taylor
commented
1 year ago In 3vyk, Reduce2 has no hydrogen on the O4 NAG B 3 (which is shown as blue rather than red) in its kinemage. (It also has no hydrogen on the O6 NAG.)
As a result, it finds the best solution to be doubly protonating the histidine.
russell-taylor
commented
1 year ago (done) The other 2 examples are 1dfu 75 2'OH to His 88 (which Reduce2 handles by double deprotonation fothe His and rotating the H attached to 75 out of the way, see image below) and 1Lnt base 8 N7 to a water OH (which Reduce2 cannot run because of missing restraints).
The Flipkin generating using the online MolProbity for 1LNT run on 7/12/2023 shows hydrogen bonding rather than clashing, so perhaps this has bug has been fixed or perhaps it broke in a newer version than is online:
russell-taylor
commented
1 year ago Checking using the online MolProbity on 7/20/2023 shows that the Flipkin is now indicating a hydrogen bond rather than a clash in the original 3vyk His 225 case:
Jane writes in an email on 2/7/2023: Serendipitously, 3vyk turned out also to exemplify two bugs, one of which Christopher & I had already found in RNA structures. That one is isolated cases of a perfect Hbond that is instead shown as a clash (!?X@!). View 3 in the 3vyk multikin shows this between an OH on NAG 3 and an unprotonated Ne2 on His 225.
(done) Check Reduce2 behavior.