Dear Xplor-NIH developpers, I plan to use the PASD/MARVIN facility in the Xplor-NIH structure determination package to calculate the structure of a protein from solid state data. PASD seems to me to be very ideal for that task, since the experimental data from solid state spectra is very sparse and noisy presenting a challenging problem. The main source of information from solid state data is an 13C-13C dipolar correlation experiment containing cross peaks between carbon pairs close in space (conseptually similar to NOESY). This I plan to use do derive broad distance bounds.
My question is can I use this type of 2D CC data in PASD? - what would be the syntax of the "NOE-files"? I cannot find any example of NOE data in the eginput/marvin/* subdirectories of the Xplor-NIH distribution, where should I look for it? Does a python interface to PASD exist? One of the main challenge to solid state structure is the presense of intermolecular contact (i.e. CC interactions). This leads to cross peaks not being consistent with a monomer structure. Furthermore these contacts would tend to be systematic rather than random which might result in non-averaged "noise"-peaks. How do you think PASD will perform? I plan to also perform calculations for a dimer model system (modeling monomer interactions in the solid state), for this system PASD should be able to identify which contact are intra- and intermolecular - I hope... Can I use an NCS (to enforce identity of the monomers) potential energy term as well from the tcl interface? What about distance difference potential to enforce NMR equivalence of the monomers? I hope you can help me answer my questions. Best regards, Jakob Nielsen
