To those in the same spot, the fix was to first run this: http://kinemage.biochem.duke.edu/software/remediator.php
And then remove all the H's and let your favorite refinement software put them back: grep -v " H" 52remediated.pdb > 52remediated_noH.pdb Sorry for bothering those of you who are already more up-to-date! ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu<mailto:pr...@uchicago.edu> ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phoebe A. Rice [pr...@uchicago.edu] Sent: Thursday, February 19, 2015 8:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Thymine methyl in coot When trying to adjust the "chi" angles of a dT in coot 0.8.1, the methyl and its H's (which I called C5M to make phenix happy) rotate with the sugar, producing a rather base bizarre geometry.
