Wont coot fix the nomenclature issue, then you can check whether you have
a real chirality problem - eg a squashed flattened VAL..

Eleanor


On Fri, 6 Jan 2012 09:47:15 -0600, Katherine Sippel
<[log in to unmask]> wrote:
> Incidentally the PDB validation server will spit out similar errors if
you
> have hydrogens on lysine side chains (also not a chiral center) should
they
> get swapped upon regularization during refinement. It makes the chemist
in
> me cringe a little bit.
> 
> Katherine
> 
> On Fri, Jan 6, 2012 at 8:30 AM, Robbie Joosten
> <[log in to unmask]>wrote:
> 
>>  Hi Afshan,
>>
>> I assumed, because you mentioned only VAL and LEU, that you were
refering
>> to the CB (VAL) and CG (LEU) as problematic chiral centers. Paul is
right
>> that these atoms are not chiral in a chemical sense, but they are in a
>> computational sense because every connected atom has a unique name. The
>> PDB
>> is pretty strict in this sense (as it should be), but they could/should
>> call it a nomenclature error. They could also just swap the atom names
>> like
>> I described and solve the problem for you. Anyway, please give a bit
more
>> details about your problem.
>>
>> Computational chirality problem can be a serious problem for
refinement:
>> if the chirality is wrong due to swapped atom names, the chiral volume
>> restraint will try to invert your chiral center. This can lead to
>> malformed
>> geometry, typically flattening of of the group. This means that a
>> computational chirality problem can lead to a 'real' chirality problem.
>> In
>> Refmac, this will not happen for LEU or VAL, but it will happen for
>> things
>> like SO4, GOL, and a whole lot of other more interesting hetero
>> compounds.
>>
>> @ Paul, I don't think it will be a CCP4 program that reported the
>> problem.
>> Does the 'fix nomenclature problems' option in Coot also do VAL and
LEU?
>>
>> Cheers,
>> Robbie
>>
>>  ------------------------------
>> Date: Fri, 6 Jan 2012 10:44:58 +0000
>> From: [log in to unmask]
>> Subject: Re: [ccp4bb] chirality problem
>>
>> To: [log in to unmask]
>>
>> Hi Afshan,
>>
>> This is not the solution if you are right about the problem being one
of
>> chirality (and it is if it is not and is merely an issue of
nomenclature
>> (as I suspect is the case)).  So the question is, if the problem is
>> indeed
>> one of nomenclature, what software (if any) described it as a chirality
>> issue?  If it is one of ours we should fix that.
>>
>> Paul
>>
>>
>> On 05/01/12 11:44, Robbie Joosten wrote:
>>
>> Hi Afshan,
>>
>> Just swap the (names of) the CD and CG atoms, no need for refinement.
The
>> CCP4 dictionary allows both chiralities for LEU and VAL, so Refmac
won't
>> detect the problem. The problem is still very real to many programs so
it
>> should be fixed.
>>
>> Cheers,
>> Robbie Joosten
>>
>> ------------------------------
>> Date: Thu, 5 Jan 2012 02:46:30 -0800
>> From: [log in to unmask]
>> Subject: [ccp4bb] chirality problem
>> To: [log in to unmask]
>>
>>  Dear Users,
>>
>> I am facing difficulties to validate my structure according to PDB
>> server.
>> I have solved my structure and now want to submit in PDB but during
>> validation process i have  some chirality problem specially   VAL and
LEU
>> amino acids there are total 18 amino acids which deviated from the
>> chirality so how can i solve this problem.
>>
>> Any suggestion would be highly appreciated.
>>
>>
>> Best Regards
>>
>> AFSHAN
>>
>>
>>