Subject: Re: [nmr_sparky] changing axis w#
From: Andrew Olson
Date: Dec 7, 2009

Previous: 636

if you want to get the same nomenclature is you use in sparky you have to
supply those names in sparkynames. prot (see translate.cya)

Eiso

I dont quite understand this! I cant use the output .prot file from CYANA for this? Where can i get the translate.cya macro?

--- On Wed, 12/2/09, eiso e.ab@... wrote:

From: eiso e.ab@...
Subject: Re: [nmr_sparky] changing axis w#
To: nmr_sparky@yahoogroups.com
Date: Wednesday, December 2, 2009, 9:30 AM

Andrew Olson wrote:


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



the empty lines are alternative( or ambiguous) assignments to the same NOE
since sparky has no possibility for ambiguous assignments you have to decide
what you want to do with this. if you delete the lines with space youll select
on of the possible assigments, not guarantee that is the correct or most likely one.

you could keep them unassigned and store the possible assignments as a peak note

or use this:
http://www.nmr. chem.uu.nl/ ~eiso/bin/ peaks2sparky. awk

peaks2sparky. awk protein.seq sparkynames. prot noe.peaks sparkypeaks. list

if you want to get the same nomenclature is you use in sparky you have to
supply those names in sparkynames. prot (see translate.cya)

Eiso