Subject: Re: [nmr_sparky] sparky-mars
From: Vitaliy Gorbatyuk
Date: Dec 20, 2005

Previous: 56 Next: 58


Thank you Josh.
I think what I was asking is how people do the input files for the second,
third, etc. run of Mars.
After the first run we get these files: sparky_CO.out, sparky_CO-1.out, etc.
As it is suggested in the MARS paper, I read in the peaks from
sparky_CO-1.out into HNCO spectrum with Sparky rp command. Similarly, I
read other sparky_*.out files into the corresponding specta. Then, I use a
strip tool to build a sequence of strips and visually analyze the sequential
assignment obtained in the first run of MARS. After the analysis I want to
run MARS for the second time. But the name format of the peaks is
CO,Co,CA,Ca, and so on. Thus, I have to go to the spectra where I have
manually done peak picking of pseudoresidues and where the peak names are
CO, CO-1, CA, CA-1, and so on, and perform corrections there: add news
peaks, delete wrong peaks, correct typos, which all this was found during
the analysis of strips. After corrections, I again save a peak table with
tb command, modify fix_con.tab, fix_ass.tab and run MARS the second time.

Thus, basically I have two sets of the same triple resonance spectra in
sparky format (two sparky projects if you wish). One was used to do peak
picking and assigning the spin systems. Another was used to read in peaks
from MARS sparky_*.out files and to verify/correct the MARS sequential
assignment and my mistakes/typos. I consider this approach a bit cumbersome
and wonder if someone has a better one.

In this regard, did anyone think on how to delete a Sparky project without
going in all Sparky directories, finding proper files and delete them
manually?

Cheers,
Vitaliy


From: Josh Ward wardjm@...
Reply-To: nmr_sparky@yahoogroups.com
To: nmr_sparky@yahoogroups.com
Subject: Re: [nmr_sparky] sparky-mars
Date: Mon, 19 Dec 2005 10:06:11 -0500
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





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