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.