Hello Charlies,
I have a look at your macro and wonder why you need to use FT and SP for z dimension 3 times of each? Once, by mistake I used 2 times for FT (or SP, dont remember) in one dimension and I got distorted spectrum. After remove one of them, I got the normal spectrum again. Also, is this recommended to use HT and FT together? Could you share the advantage that Hilbert Transform and Fourier Transform combination gives?
Have you tried to use the template macro for processing 3D data quite in NMRPipe? From your macro, suppose the phases are correct (I dont see the phase correction of z dimension in your macro, may be you dont need it), I got a version as below
xyz2pipe -in data/test%03d.fid -x -verb
| nmrPipe -fn SOL
| nmrPipe -fn SP -off 0.35 -end 0.99 -pow 2 -c 0.5
| nmrPipe -fn ZF -auto
| nmrPipe -fn FT
| nmrPipe -fn PS -p0 -142.0 -p1 0.0
| nmrPipe -fn EXT -x1 11.0PPM -xn 6.0.0PPM -sw
| nmrPipe -fn POLY -ord 1
| nmrPipe fn TP
| nmrPipe -fn LP -fb
| nmrPipe -fn SP -off 0.45 -end 0.99 -pow 2 -c 0.5
| nmrPipe -fn ZF -auto
| nmrPipe -fn FT
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di
| nmrPipe -fn POLY -ord 1
| pipe2xyz -out FT2/test%03d.ft3 -y ov
xyz2pipe -in FT2/test%03d.ft3 -z -verb
| nmrPipe -fn LP -ps0-0
| nmrPipe -fn SP -off 0.5 -end 0.9 -pow 1 -c 0.5
| nmrPipe -fn ZF
| nmrPipe -fn FT
| nmrPipe -fn POLY -auto
| pipe2xyz -out FT2/test%03d.ft3 -z ov inPlace
xyz2pipe -in FT2/test%03d.ft3 -out gc_co_nh.ft
pipe2ucsf gc_co_nh.ft gc_co_nh.ucsf
Hope it helps :)
Hoa
From: nmr_sparky@yahoogroups.com [mailto:nmr_sparky@yahoogroups.com]
On Behalf Of charles_stevens@...
Sent: Wednesday, December 12, 2012 10:11 PM
To: nmr_sparky@yahoogroups.com
Subject: [nmr_sparky] Re: Trouble with converting to UCSF format from Pipe
Hello Andrew and Hoa,
Thank you for your replies.
I have tried both methods that you had suggested and the result is the same as what I was getting from my original inputs.
Here is a link to a comparison screenshot of the same data in Sparky nmrDraw (showing the same plane at 113.9 ppm in the 15N dimension )
I have used the same methods that I had mentioned before for the hcacb, and cbccaconh spectra in this dataset with no problems.
In case it helps, here is the macro for the data processing for the cc(co)nnh data:
var2pipe -in ./fid -noaswap -aqORD 1
-xN 1024 -yN 144 -zN 64
-xT 512 -yT 72 -zT 32
-xMODE Complex -yMODE Complex -zMODE Rance-Kay
-xSW 8384.865 -ySW 10056.517 -zSW 2025.983
-xOBS 499.861 -yOBS 125.695 -zOBS 50.656
-xCAR 4.726 -yCAR 46.013 -zCAR 118.006
-xLAB HN -yLAB C -zLAB N
-ndim 3 -aq2D States
-out ./data/test%03d.fid -verb -ov
xyz2pipe -in ./data/test%03d.fid -x -verb
| nmrPipe -fn SOL
| nmrPipe -fn SP -off 0.35 -end 0.99 -pow 2 -c 0.5
| nmrPipe -fn ZF -auto
| nmrPipe -fn FT
| nmrPipe -fn PS -p0 -142.0 -p1 0.0
| nmrPipe -fn EXT -x1 11.0PPM -xn 6.0.0PPM -sw
| pipe2xyz -out FT2/test%03d.ft2 -x
/font
xyz2pipe -in FT2/test%03d.ft2 -z -verb
| nmrPipe -fn SP -off 0.5 -end 0.9 -pow 1 -c 0.5
| nmrPipe -fn ZF -zf
| nmrPipe -fn FT -di
| pipe2xyz -out FT2/test%03d.ft2 -z -inPlace
xyz2pipe -in FT2/test%03d.ft2 -y -verb
| nmrPipe -fn LP -fb
| nmrPipe -fn SP -off 0.45 -end 0.99 -pow 2 -c 0.5
| nmrPipe -fn ZF -auto
| nmrPipe -fn FT
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di
| pipe2xyz -out FT2/test%03d.ft2 -y -inPlace
xyz2pipe -in FT2/test%03d.ft2 -z -verb
| nmrPipe -fn HT
| nmrPipe -fn FT -inv
| nmrPipe -fn ZF -zf -inv
| nmrPipe -fn SP -off 0.5 -end 0.9 -pow 1 -c 0.5 -inv
| nmrPipe -fn LP -ps0-0
| nmrPipe -fn SP -off 0.5 -end 1.0 -pow 2 -c 0.5
| nmrPipe -fn ZF -auto
| nmrPipe -fn FT -di
| nmrPipe -fn POLY -auto
| pipe2xyz -out FT3/test%03d.ft3 -z -inPlace
xyz2pipe -in FT3/test%03d.ft3 -x -verb
| nmrPipe -fn POLY -window 4 -ord 1
| pipe2xyz -out FT3/test%03d.ft3 -x -inPlace
xyz2pipe -in FT3/test%03d.ft3 -y -verb nbs p;
| nmrPipe -fn POLY -window 4 -ord 1
| pipe2xyz -out FT3/test%03d.ft3 -y -inPlace
xyz2pipe -in FT3/test%03d.ft3 -x gc_co_nh.ft3
pipe2ucsf gc_co_nh.ft3 gc_co_nh.ucsf
Thank you again for all of your help,
-Charlie
--- In nmr_sparky@yahoogroups.com, Do, Quynh Hoa q.h.do@... wrote:
Hello Charlie,
Did you check again other part of your macro?
Here is the code that I used to convert Pipe format to UCSF format. It works and gives nice spectra.
xyz2pipe -in ft/test%03d.ft3 -out NCOCX.ft
pipe2ucsf NCOCX.ft NCOCX.ucsf
Good luck,
Hoa Q. Do
From: nmr_sparky@yahoogroups.com [mailto:nmr_sparky@yahoogroups.com] On Behalf Of charles_stevens@...
Sent: Tuesday, December 11, 2012 10:57 PM
To: nmr_sparky@yahoogroups.com
Subject: [nmr_sparky] Trouble with converting to UCSF format from Pipe
I am having trouble with importing two 3D spectra into sparky. when I open the processed (h(cco)nh cc(co)nh) data in nmrD raw, the files look great, but after converting it to ucsf format using the following command:
xyz2pipe -in FT3/test%03d.ft3 -x ghc_co_nh.ft3
pipe2ucsf ghc_co_nh.ft3 ghc_co_nh.ucsf
the spectra in the output files are distorted. Peaks do not appear where they should when comparing the nmrDraw and Sparky side by side, and in the case of the cc(co)nh the peaks appear to be out of phase (negitave smear to the left, and positve smear to
the right).
I was wondering what I should try to solve this problem.
Thanks!
-Charlie
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