Yes (indeed), the CG of a LEU is not a chiral centre - and thus is not
refined/optimised. If the the CDx atoms are misassigned, then that is
what we call a "nomenclature error" (I think I got the terminology from
Refmac).
The last chi angle of residues types TYR, PHE, ASP and GLU used to be
checked against for IUPAC convention and thus we used to see a
nomenclature error for those residues as an outlier in the rotamer graph
[1]. VALs and LEUs are not checked in this way for the rotamer graph.
However, there is a tool to fix nomenclature errors, and VALs and LEUs
are checked there. Have a look in the manual about this:
http://www.ysbl.york.ac.uk/~emsley/coot/doc/user-manual.html#SEC146
In the terminal, it will tell you all the nomenclature errors that it
found and fixed - i.e. there is no tool in Coot that will just tell you
about nomenclature errors without fixing them too.
This tool is not available in the GUI - it should be trivial to add an
extension. I will make a note to do so.
Thanks,
Paul.
[1] that was before we moved to the Richardson rotamer probability
library, that has yet to be rationalised.
Dale Tronrud wrote:
Yes, real space refinement takes into account stereochemical
restraints, that is what all the traffic lights are about.
What, exactly, is the PDB complaining about? If it is the
chirality of atom CG, then you should realize that this is not
a real chiral center. CG becomes chiral when the two CD atoms
are given numbers. There are two ways to do it but a convention
has been adopted to make all Leu CG atoms look the same. If
your residue is being flagged as backwards, simply edit the PDB
file and swap the numbers on the two CD atoms.
Some programs monitor fake chiral centers but others do not.
The PDB certainly does, at least for amino acids. Check the
labeling of oxygen atoms in phosphates if you want a scare.
If this isn't your problem please add details.
Ha! Have you been talking to Gert Vriend :)
Dale Tronrud
Francis E Reyes wrote:
Actually i just checked my structure with the Validate -> Incorrect
Chiral Volumes. It seems to check out OK, but the PDB doesn't like it?
Anyone?
thanks
FR
On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote:
Hi all,
Just tried to submit a PDB and it seems that LEU is not correctly
positioned (CG/CD1,CD2). I real space refined this residue, does the
real space refinement take into account stereochemical considerations?
Thanks
FR
