I found the answer to my quetion...i had to use -321 flag while using ucsfdata to alter the w# for each axis.
I do have another question however regarding cyanagarant2sparky. The output xeasy files give spaces like this
272 4.350 6.699 55.453 4 U 9.953E+06 0.000E+00 e 0 0 0 0
273 3.097 10.229 55.130 4 U 6.908E+07 0.000E+00 e 0 0 0 0
274 3.990 8.415 55.374 3 U 4.592E+07 0.000E+00 e 0 906 918 903 #VC 0.46404 #QU 0.300 #SUP
0.71
906 932 903 #VC 0.53596 #QU 0.580 #SUP 0.71
275 4.290 7.844 55.390 4 U 2.010E+07 0.000E+00 e 0 0 0 0
276 4.291 7.730 55.348 4 U 1.623E+07 0.000E+00 e 0 0 0 0
277 3.804 8.432 54.704 4 U 1.857E+07 0.000E+00 e
0 0 0 0
278 4.033 7.954 54.784 4 U 4.022E+07 0.000E+00 e 0 0 0 0
279 3.165 10.287 54.263 4 U 2.409E+08 0.000E+00 e 0 0 0 0
280 4.284 8.155 54.283 3 U 3.424E+07 0.000E+00 e 0 113 118 110 #VC 0.40458 #QU 0.316 #SUP
0.55
113 128 110 #VC 0.59542 #QU 0.348 #SUP 0.55
281 3.118 9.335 54.148 4 U 3.189E+07 0.000E+00 e 0 0 0 0
Im not sure how to interpret these, any help with that would be appreciated but my real question is, cyanagarant2sparky will not work if these spaces are in there. I had to delete the spaces on the output xeasy file from cyana to get this to work. Is this ok to delete those spaces, or should
the whole peak be deleted? Thanks
--- On Tue, 12/1/09, Jinwon Jung jinwon.jung@... wrote:
From: Jinwon Jung jinwon.jung@...
Subject: Re: [nmr_sparky] changing axis w#
To: nmr_sparky@yahoogroups.com
Date: Tuesday, December 1, 2009, 11:53 AM
Hi Andrew,
CYANA automatically detects axis from their chemical shift and some
assignments given by user.
If it does not work, something is wrong with you peak list.
You may try declare axis in the header of file like this:
# Number of dimensions 3
#FORMAT xeasy3D
#INAME 1 HC
#INAME 2 H
#INAME 3 C
#CYANAFORMAT HhC
0 4.453 4.453 70.302 1 U 9.707E+02 0.000E+00 e 0
0 0 0
1 4.454 4.306 70.314 1 U 1.984E+02 0.000E+00
e 0
0 0 0
2 4.453 1.084 70.278 1 U 2.191E+02 0.000E+00 e 0
0 0 0
3 4.014 6.971 68.349 1 U 2.701E+01 0.000E+00 e 0
0 0 0
....
HC and capital H mean proton attaching on carbon.
For the second case, I have no idea. please give more information
about your situation.
Showing the result of ucsfdata will be good like this:
% ucsfdata cactd_c_noesy. ucsf
axis w1 w2 w3
nucleus 1H 13C 1H
matrix size 512 128 1461
block size 16 4 45
upfield ppm -2.304 47.694 -1.004
downfield ppm 11.704 87.634 9.001
spectrum width Hz 12610.340 9041.591
9007.310
transmitter MHz 900.280 226.375 900.280
Jinwon
:: Jung, Jinwon. Ph.D.
:: 정진원(鄭鎭沅)
:: Department of Structural Biology
:: University of Pittsburgh
:: 3501 FIFTH AVE BST3 B040
:: PITTSBURGH PA 15260
:: USA
:: Tel:+1-412-383- 6939
:: Fax:+1-412-648- 9008
On Nov 30, 2009, at 9:56 PM, Andrew wrote:
I would like to change the axis of my C13 NOESY so that the carbon
dimension is w3 instead of w1. I think this is causing my issues
with CYANA not reading any peaks...either that or my calibration is
wrong :(
Also can i only pick peaks in part of a 3D spectra say only 2 or 3
ppms but in every plane? Thanks
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