Hi,
The eginput doesn't contain any examples, but it's a simple
modification to the initMatch scripts.
1. Add the line
package require nmrstar
to the top, along with the other 'package require' lines.
2. Change the line
set shifts [readPippShiftTable -fileName cvn_c13noe.shifts -
remarksVariableName saRemarks] ; noOutput
to
set shifts [readNMRSTARShiftTable -fileName aFile.str -
remarksVariableName saRemarks] ; noOutput
A caveat--very few NMR-STAR formatted shift tables have correct
ambiguity codes (see http://www.bmrb.wisc.edu/elec_dep/gen_aa.html),
and this can create big problems reading tables that have even simple
ambiguities, like non-stereo methylenes.
Another caveat--most NMR-STAR formatted shift tables also use oddball
atom names (e.g., calling a lysine's beta protons HB2 and HB3, even
though valine's methyls are named CD1 and CD2). I haven't found
proper documentation of how or why these names are generated, so I
can't correct them automatically. If someone from the Wisconsin
group (hi Gabriel!) could give me a pointer, I could fix this in a
future
version. But for now, you have to correct the NMR-STAR file's atom
names by hand.
Also note that Marvin can only read NMR-STAR shift tables. I have
yet to see an NMR-STAR formatted NOE peak table. Again, if someone
could provide an example, I could update the code.
Hope this helps.
--JK
On Apr 2, 2007, at 2:23 PM, Jeff Ellena wrote:
Hi,
Are there any examples of reading BMRB NMR-STAR chemical shift
files into xplor-nih for use with PASD? If yes, where are they? If
no, what is the correct syntax for reading BMRB NMR-STAR chemical
shift files?
Thanks,
Jeff Ellena
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