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
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