Hi Emmanuel,
The monomer library is great, but it is also created by scientists (and
computers) that can err. I remember a few cases (some reported on the
ccp4bb) where mistakes were revealed and later fixed. Just because
something is in the monomer library that does absolve anyone from not
checking their ligands. And that still should not decrease our
appreciation of scientists for the selfless task of creating the monomer
library that ships with ccp4 and phenix.
Another great resource is Gerard Kleywegt's HIC-UP. In the cases where I
suspected the monomer library of having errors, HIC-UP had the right
geometry. In this case, "Get Monomer"ing DTT and downloading HIC-UP's
DTT give me opposite chiralities on C3. I don't know which one is true,
but I suspect HIC-UP is. You can download restraint files through links
(to prodrg, I believe) from HIC-UP.
Cheers,
Engin
On 11/25/10 8:38 AM, Linda Schuldt wrote:
Hi Emmanuel,
it is hard for me to imagine that Coot has the wrong stereoisomer. So what
I think might have happend is the following:
You have imported the correct DTT, but when you have fitted the molecule
into the map you might have distorted the sterochemistry at the C3 atom.
And then it was refined like that. I had once a similar observation with
MPD. Did you insert the three DTT molecules individually, or did you "copy
and paste" the same molecule around (which might explain why you have it
for all three)?
And why don´t you just import DTT into Coot and check yourself if it has
the correct sterochemistry. This is a fast and easy way to find out if
something is wrong in your Coot library.
Unless you have very high resolution which clearly shows that you have DTU
instead of DTT, I would change your coordinate file to DTT and send it
again to the pdb.
Hope this helps you.
Best wishes,
Linda
Emmanuel Saridakis schrieb:
Dear All,
Possibly a trivial question but your experience would be much appreciated:
I recently submitted a structure to PDB containing 3 DTT (dithiothreitol)
molecules, or so I thought. The molecules had been imported and fitted
with Coot using the Get Monomer... instruction with the code DTT. The
Annotator responded, quite rightly as it turns out, as follows:
Please note DTT in your coordinates has been changed to DTU since it
has incorrect stereochemistry as DTT.
Please review the stereochemistory in the attached validation report
summary.
You can send me corrected stereochemistry for DTT if you want it
changed back.
DTU (2R,3S)-1,4-disulfanylbutane-2,3-diol
C4 H10 O2 S2
DTT (2R,3R)-1,4-disulfanylbutane-2,3-diol
C4 H10 O2 S2
So, is the "DTT" monomer of Coot in fact its stereoisomer known as
dithioerythritol? Should I import the correct DTT from elsewhere and
re-refine or is there something else behind this?
Thanks a lot for any suggestions!
Emmanuel
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
