Subject: Re: sparky-mars
From: ethernet3399
Date: Dec 21, 2005

Previous: 58 Next: 60


Dear Vitaliy Gorbatyuk,
I encountered the situation you mention.

I didnt read the sparky_CO-1.out into sparky HNCO spectrum.

While I notice the MARS program is written with awk language, so you
can adjust the source code to make it output the CO-1, not
the Co. Can it fix your problem?

By the way, I agree with what Josh Ward says. I just rename the
residues name, such as PR1--A35, while leave the CO-1 atom
name unchanged. After all the MARS iteration finished, then we can
rename the CO-1 atom name to T34 CO.

Of course, if youd like to change the MARS source code, please let
the MARSs author know.

Or if you have any problem to rewrite the MARS awk source code, we
can exchange idea about that further.

Tieying Zhang
at SIBS


--- In nmr_sparky@yahoogroups.com , Vitaliy Gorbatyuk
vitaliy_gor@h... wrote:

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@p...
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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