Subject: Re: [nmr_sparky] sparky-mars
From: Josh Ward
Date: Dec 19, 2005

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I am not exactly sure what you find so weird in the MARS formats, but
here is the general strategy that I use when running assignments with MARS.

I first manually label pseudoresidues in sparky using 15N-HSQC, HNCACB,
and CBCA(CO)NH (I have not performed CO assignments yet for my
protein.) I label each pseudoresidue, giving a number for the group, N
and H for the backbone amide resonances, and CA, CA-1, CB, and CB-1
carbon assignments.

I then save the assignment table after this [Peak - Assignment -
assignment table (at)] and feed this table into MARS as input.

After running MARS, I print out the assignment table and the MARS output
file assignment_AAs.out and use the hardcopies at the computer to go
through and manually verify the MARS assignments.

After verification I use the rename resonances (rr) facility to change
the group names to resonances (ie. 1 -- A35, 2 -- E26, etc), and the
CA-1 and CB-1 atoms to match the appropriate i-1 residue. I admit, this
process is tedious, and I am looking for a way to automate it (I would
like to write a python extension to automate the renaming process but
havent yet found the time.)

Anyway...my two cents. :) Hopefully it makes sense, or helps, or at
least shows you you might not be doing it the hardest way. ;)

ibmvg wrote:

Hello,

I wonder if somebody could share their way of working with Sparky-MARS
tandem on the backbone assignment. I do not like how I do it. Making
the input for MARS is straightforward, however tedious. But MARS output
with all these Co, Ca, etc. seems to be weird since it differs from
both MARS input and IUPAC format. Thus, in addition to a set of spectra
where we pick NMR peaks and give them names in the format of MARS
input, one has to also have a set of all spectra for reading in the
MARS output. This set of spectra with peaks from MARS output I use for
manual verification of MARS assignment. Then, I use the first set of
spectra with CO, CO-1, etc. format to correct/add those mistakes/peaks
which I found in the second set of spectra using MARS output result. It
seems to me a cumbersome way. Maybe I am missing some neat trick which
could significantly simplify the job.

ANY ideas/suggestions are welcome :)!

Thanks & Merry Xmas!







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--
Josh Ward
Graduate Research Assistant
Purdue University
Department of Medicinal Chemistry and Molecular Pharamacology
Lily Hall of Life Sciences
Phone: (765) 494-2191