 |
 |
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 > > >