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