[ccp4bb] Thymine methyl in coot

[Phoebe A. Rice]

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.

Re: [ccp4bb] Thymine methyl in coot

[Paul Emsley]

On 19/02/15 21:03, Phoebe A. Rice wrote:
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.




Hello Phoebe,

I suspect things are going wrong because C7 is called C5M in your pdb file.

I think dTs should be now DTs in Coot.

Paul.

p.s. "chi" - yes :-/

Re: [ccp4bb] Thymine methyl in coot

[Phoebe A. Rice]

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.