Francis:

 

When I had a similar issue, Paul told me that one had to mutate a residue to be sure that the stereochemistry is correct.  Moreover, as of the last time I checked with Paul, COOT does look at the chiral volumes for pseudo-chiral centers such as Leu and Val, so it is no surprise that COOT doesn't catch it.

 

Try either Simple Mutate or Mutate & Auto Fit …

 

Steven

 

>-----Original Message-----

>From: Mailing list for users of COOT Crystallographic Software

>[mailto:[log in to unmask]] On Behalf Of Francis E Reyes

>Sent: Thursday, March 05, 2009 6:36 PM

>To: [log in to unmask]

>Subject: Re: stereochemical violations in real space refinement?

> 

>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

>> 

>> ---------------------------------------------

>> Francis Reyes M.Sc.

>> 215 UCB

>> University of Colorado at Boulder

>> 

>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

>> 

>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

> 

>---------------------------------------------

>Francis Reyes M.Sc.

>215 UCB

>University of Colorado at Boulder

> 

>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

> 

>8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D