Hi Charles, Thank you. Both approaches make sense, and I think I will give the gyroA method a go. And yes, the advisory is appreciated and one I've considered. Luckily, I'm looking at a metalloprotein (no tag flexibility) and the tensors derived independently from RDCs and PCSs found a Xax within 0.5 (*10^-32 m^3). So the approximation of a single tensor isn't unreasonable in this case, I think. Best, John
On Wed, May 6, 2020 at 4:43 PM Charles Schwieters <[email protected]> wrote: > > Hello John-- > > > > > I'm looking to perform a refinement with a combination of PCSs and > > paramagnetic induced RDCs. Ideally, I would like to use a single > tensor object > > to describe them (i.e. have the Xax, Xrh, Euler Angles shared between > PCSs and > > RDCs) > > > > If I write something as shown below, the Da would be properly set for PCS > > refinement... but this would be much too large for the RDC restraints. > > The relationship between Xax and Da should be something as follows: > > Dax = ((Xax)/(30*u0*k*T))*(Bo**2*39.46) > > *If* the alignment tensors are indeed the same aside from scaling, you > can set this factor using the gyroA member of RDCPot, either the one > corresponding to PCS data, or the one for RDC data, e.g. > > for M in Metals: > Para_Pot = PotList('Para_{}'.format(M)) > Restraint = '{0}_NH_PCSs'.format(M) > PCS_File = 'PCS_tbl_Files/{0}_NH_PCSs.tbl'.format(M) > pcs_restr = create_RDCPot(Restraint, PCS_File, Metal_Tensors[M]) > pcs_restr.setUseDistance(True) > pcs_restr.setGyroA( FACTOR ) > ... > > However, as my colleague Guillermo Bermejo points out: > > I think it might be relevant to ask whether there's motion involved > in the paramagnet (e.g., flexible tag). If so, I believe the > effective tensor involved in the PCS and RDC data might be > different, because the two types of data average differently, so > forcing the same tensor on both datasets may not be the right way to > go. > > It is also possible to set as the same the orientation and rhombicity > of two different tensors - allowing the Da only to vary. There's an > example of this approach in eginput/dna_refi/ensemble.py in the > Xplor-NIH distribution. > > best regards-- > Charles > -- *John B. Stiller* Ph.D. Candidate Kern Group Department of Biochemistry Brandeis University ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
