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 <[email protected]> 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 > <[email protected]>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: [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 >> >> >>
