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: [email protected] Subject: Re: [ccp4bb] chirality problem To: [email protected] 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: [email protected] Subject: [ccp4bb] chirality problem To: [email protected] 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
