The REFMAC option of NCS Local restraints checks how closely your subunits match and adjust the spans of residues restrained accordingly. So if a helix has moved relative to the main body of the molecule, restraints will still be applied but with an adjusting fit.
That works very well in general. And of course since the sequences of E & F are different no restraints will be called for Eleanor On 17 April 2015 at 05:41, Robbie Joosten <[email protected]> wrote: > The modern implementations of local NCS restraints are quite forgiving > when it comes to structural differences, so normally they work very well > with very little risk. > In a practical CCP4 sense: Just switch on local NCS restraints in Refmac. > They will do the trick. Using those is also the default in pdb_redo and it > really helps a lot. > > Cheers, > Robbie > > Netherlands Cancer Institute > Http://xtal.nki.nl/PDB_REDO > > Sent with my Windows Phone > ------------------------------ > Van: Smith Liu <[email protected]> > Verzonden: 17-4-2015 06:03 > Aan: [email protected] > Onderwerp: Re: [ccp4bb] on NCS restraint > > Dear Jurgen, > > My understanding is that NCS restraint can significantly enhance the speed > of calculation, but considering the subunits even with the eactly same > sequence may not be identical, to have NCS restraint may be not necessary > or may be not good for the refinement, am I right? > > Smith > > > > > > At 2015-04-17 09:09:05, "Jurgen Bosch" <[email protected]> wrote: > > yes. > Have two sets of NCS operators one that describe the four subunits and one > describing the two subunits. If during the refinement of your structure you > should find out that the subunits are not identical to each other you can > relax the NCS weights. > > Jürgen > ...................... > Jürgen Bosch > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://lupo.jhsph.edu > > On Apr 16, 2015, at 9:02 PM, Smith Lee < > [email protected]> wrote: > > > Dear All, > > If a protein contains 6 subunits, 4 subunits from the same sequence > (subunit A, B, C, D all from the same sequence), each of the 2 other > subunits from 2 diffrent sequences (subunit E from the second sequence, > subunit F from the third sequence), in this situation should I use NCS > restraint or not? > > If my protein contains 2 subunits, both of the 2 subunits composed of the > eaxctly same sequence, however supposing the 2 subunits have a little > diffrent conformation, in this situation should we use NCS retraint or not? > > Smith > > > > > > >
