Re: [ccp4bb]: Refmac vs. cns: nucleic acids?

[Phil Evans <pre@mrc-lmb.cam.ac.uk>]

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As far as I can see, it is always wrong to restrain ring-puckers in
sugar rings. The whole point of model building & refinement is that
you don't know the conformation in advance. It's also not necessary,
even at low resolution, since the ring pucker is well-determined by
the lever action of the base at one end and the 5' substituent at the
other.

For some reason, these torsion restraints have crept in to a lot of
dictionaries distributed for Xplor, CNS, O & probably other programs.
It has not been a problem with Refmac I think, because the distributed
dictionaries have not included torsion angle restraints.

This also of course  applies to other sugar, single nucleotides etc
(eg ATP, NAD). Also the O dictionary for Pro.

Phil

(don't you just love these flame wars . . . )


Anastassis Perrakis writes:
 > Phoebe Rice wrote:
 > 
 > > 
 > > I'd be interested in people's humble opinions on their experiences with 
 > > nucleic acids in particular.  Many of the backbone torsion angles aren't 
 > > well defined in moderate-resolution maps (2.5ish), but they do matter.  
 > > Especially for non-canonical structures, I've wondered if we're really 
 > > dealing with them properly.
 > 
 > Since nobody picked up on that yet, here I go ... i hope I will be 
 > humble enough [;-)]
 > 
 > The word is that XPLOR/CNS is far better than REFMAC on refining nucleic 
 > acids. REFMAC (.. and PROLSQ back then) make the sugar backbone 'funny' 
 > according to some, the bases non-planar according to others.
 > 
 > Partially true - I think.
 > 
 > For the non-planar bases some RTFM would suggest to adjust the WMATRIX 
 > value and for me and most others that works.
 > 
 > For the backbone though there is a point. I vaguely recall the York 
 > refinement workshop at '97. After some smart participant (Miquel Ortiz 
 > ?) pointed it out, I recall Eleanor having a look at the all-famous 
 > PROTIN code around midnight and figuring that 'main chain' could only 
 > have one chiral center - which is fine with proteins but a bit of a 
 > disaster with nucleic acids if the ribose is considered the main chain ! 
 > There was a single line fixed that I used ever since but I doubt if that 
 > ever made it in the wide public.
 > 
 > The truth now is that REFMAC5 does for sure the work properly - as 
 > properly as CNS although slightly different if I understand it correctly.
 > 
 > The trouble start when having 'unusual' DNA, i.e. bent DNA deviating 
 > from B-DNA. CNS has a HUGE energy term dissallowing sugars to change the 
 > puckering amplitude - accordign to that it seems more likely to see a 
 > Ca-C bond at 1.0 A than a sugar torsion angle change by 1 degree .... 
 > So, once your sugar was in the C2-endo conformation (thats B-DNA, just 
 > looked it up) it was staying there and the DNA looked great.
 > 
 > At 2.5 A resolution and below everybody is happy and justifiably so.
 > DNA looks fine and you cannot really distinguish sugar puckers.
 > 
 > When I was refining the MutS structure at 2.2 A, I followed the 
 > mainstream and used CNS. However, at the place of the DNA bend (almost 
 > 60 deg) I was always getting residual density near the sugar rings ...
 > I could fiddle with other torsions and get the base into density but 
 > there was some things I did not like. After some reading of W. Saenger's 
 > book, vague memories of puckering amplitudes surfaced up (from my dark 
 > past on cyclodextrins ...). The solution that we chose for modelling the 
 > kinked DNA in MUTS was to model some sugar rings around the bend in the 
 > (unusual) C3-endo conformation, characteristic of A-DNA. That was done 
 > after some fiddling with O dictionaries. Once I told CNS about it (you 
 > can nicely restrict the puckering amplitudes in whichever conformation 
 > you like through the interface), we got a much improved map and model.
 > 
 > At the same time Refmac5 had surfaced up and I got a test-drive. Refmac5 
 > would just refine the sugars to the correct C2-/C3- endo conformation 
 > since puckering amplitudes are not explicitely restrained but the 
 > allowed/disallowed values are figured out indirectly by VdW interactions 
 > (is that correct Garib ?). For reasons of personal bias I guess, we went 
 > on with Refmac5.
 > 
 > Well, I hope I bored everybody, my revenge for 3 days of reading 
 > chemistry and editing O dictionaries (I often wonder what was worse).
 > 
 > 
 > Tassos
 > 
 > PS ... Warren, I did not say ARP/wARP once either ....

 >