DTT.cif in $CLIBD_MON has explicit chiralities, assuming these are right DTT chir_01 C2 C1 O2 C3 positiv DTT chir_02 C3 C2 O3 C4 negativ
On 25 Nov 2010, at 17:11, Paul Emsley wrote: > Credit where it's due, Coot's "Get Monomer" is just a wrapper for LIBCHECK. > > If you look at the restraints for DTT after Get Monomer, you will notice that > chiral centres are both marked as "both". Using the restraints editor (or > otherwise) change them to "positive" (C2) and "negative" (C3) and everything > will be fine (you may need to flip the H2 and H3 hydrogens if you have them). > > If you wanted to use something other than LIBCHECK, you could search the > SBase monomers and prodrgify the result (search using the substring > "dithiobutane" (and "mercaptobutane" for DTU) incidentally). > > Paul > > > On 25/11/10 16:38, 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 >>> >>> >>>
