Hi, On Sep 13, 2006, at 10:05 AM, [email protected] wrote:
> 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. > Marvin is set up to handle ordinary NOESY cases smoothly, but could probably be made to work with your data without too much difficulty. > 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? Marvin ordinarily begins with a chemical shift table and a NOESY peak location table. These can be in one of several formats. In the eginput/marvin/* examples, we include PIPP formatted shift and peak tables (this is NIH, after all!). The shift tables end in .shifts, and the peak location tables end in .PCK. The first step is to run the initialMatch TCL scripts, which read the shift and peak tables for a given experiment, match up the peak locations to shift table entries within given chemical shift tolerances, estimate distance bounds, do some pre-filtering of the resulting peak assignments, and then write out two tables for the rest of Marvin to use--a shiftAssignments file, which largely reproduces the information in the input shift table, and a peaks file, which includes the location of each peak and any possible assignments that were found during the initialMatch script. Depending on the precise nature of your data, you might just be able to use those scripts unchanged. Alternatively, you could write your own .shiftAssignments and .peaks files and just use the rest of Marvin to calculate the structures. Those .shiftAssignments and .peaks files are intended to be human- readable, and the syntax is fairly obvious. One issue that might not be obvious, though, is that every single shiftAssignment must have a unique name given to it. Similarly, every peak and peak assignment must also have a unique name. If you repeat a name, you'll get an error when you try to read in the tables. > Does a python interface to PASD exist? No. It's all scripted with TCL. Fortunately, TCL is a trivial language to learn. And I don't really use too many TCL-isms outside of the code for the pre- filtering. The code that runs the structure calculations is reasonably straightforward. > > 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? Hard to say--it depends on how great a fraction of the peaks correspond to those intermolecular contacts, how many assignments we end up with for each peak (both intra- and inter-molecular), how well we can model the overall system, and so forth. > > 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? You can add any xplor-nih potentials you like during a Marvin calculation. I've done structures with NCS and distance symmetry. It's just a matter of setting up the potentials at the beginning of the sa_pass*.tcl scripts, using the classic xplor language enclosed in a TCL XplorCommand " ... " call. When you're ready to try, let me know and I'll post in more detail. --JK
