Hello Yoav-- > > I am looking for assistance with the calculation of a symmetric > homodimer (monomer = 87 amino acids), with a strict C2 symmetry > (only rigid-body translations should be allowed during the > calculation process, and the final two monomers should be identical > in structure). My input includes TALOS angle restraints, and ssNMR > distance restraints. I should stress that I have both data-sets > formatted for a single monomer, and this does result in a > semi-successful structure calculation, and I am now interested in > extending this data for a homodimer. > I am wondering if there is an example code for this case, of a > homodimer with strict symmetry (I found several partial ones, but > not a complete example and documentation of this calculation > process), including the option to specify the symmetry axis.
I suggest starting using strict symmetry- there's an example for a slightly more complicated case in the eginput/strictSym subdirectory in the Xplor-NIH distribution. > Also, I > would like to know if there is an automatic way of converting all > (or a specific subset of) dihedral angle/ssNMR distance restraints > to be ambiguous between the inter-monomer and intra-monomer, from my > current format - all data in monomer format. The dihedral restraints need only be applied to the protomer, and likely can be used unchanged. The distance restraints can likewise be used unchanged if you have no further info about which are inter- vs. intra-subunit. The only trick for using restraints in this way is that the nMono parameter of NOEPot will need to be set to 2. Please let me know if you need further pointers with this calculation. > Lastly, is there a way to give different probabilistic > weights to the different possible assignments of a specific > restraints (i.e. specify that the intra-monomer option should be > considered with 70%, and the inter-monomer with 30%)? > In normal calculations, the energy function has tight wells around each possible assignment- with equal weight. It is conceivable to come up with a different energy function. More conventionally, one might run a proper assignment algorithm - such as PASD, and in that case varying the weighting is straightforward. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
