Question

Does anyone know how, or have a resource that can assist me in processing data collected from this experiment? Thanks.

edit: I managed to get a single spectra using a new processing script from the nmrpipe manual:

nmrPipe -in test.fid \
| nmrPipe -fn POLY -time                           \
| nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 -c 1    \
| nmrPipe -fn ZF -auto                             \
| nmrPipe -fn FT -auto                             \
| nmrPipe -fn PS -p0 -12.4 -p1 0.0  -di -verb       \
| nmrPipe -fn EXT -left -sw                        \
| nmrPipe -fn TP                                   \
| nmrPipe -fn COADD -cList 0 1 -time               \
| nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 -c 1    \
| nmrPipe -fn ZF -auto                             \
| nmrPipe -fn FT -auto                             \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb         \
          -ov  -out B.ft2

The spectra looks ok, but the peak intensities seems weaker than they should be. Anyways, next I have to figure out how to get rdc values of of this data...more reading I guess haha.

Answer 1

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Hello Elio, does this post help you? There are some instructions on processing this set with nmrPipe. I unfortunately cannot suggest any other method because I've been using only nmrPipe.

One thing to look at before you run the processing script - find out how the IP/AP loop was set up during the acquisition. This is determined by the value of one experiment parameter called 'array'. That's I think where most of the confusion comes from.

edit: try removing -axis Y option.

link

answered Mar 03 '10 at 09:31

Evgeny Fadeev
577●1

updated Mar 03 '10 at 13:55

Answer 2

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Hi Evgeny, array='IPAP', phase I set it up as the man(gNhsqc_IPAP)

link

answered Mar 03 '10 at 10:57

Elio Cino
31

Hi Elio, then I hope my advice will help you. Btw, it's not really the best idea to post follow-up in the "answer space" - you can just edit your original post. I'll make this more clear in the user interface next time. Maybe for now you can move this to your original and I remove this answer later? - Evgeny Fadeev (Mar 03 '10 at 11:30)

... the reason I say that is that these follow-ups tend to dilute the relevant answers. Cheers. - Evgeny Fadeev (Mar 03 '10 at 11:36)

Hi Evgeny. Yes, I am a bit confused with how to reply properly. I see this comment section, and the answer section at the bottom. No clue how to use the forum properly...sorry. - Elio Cino (Mar 04 '10 at 04:52)

Elio, no problems, I just need to make the user interface more clear. - Evgeny Fadeev (Mar 04 '10 at 07:31)

Answer 3

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I checked the post. My processing script looks like:

nmrPipe    -in test.fid \
| nmrPipe  -fn SOL \
| nmrPipe  -fn SP -off .4 -end 0.98 -pow 2  -c 0.5             \
| nmrPipe  -fn ZF -auto                                         \
| nmrPipe  -fn FT                                               \
| nmrPipe  -fn PS -p0 -8.8 -p1 0.0  -di                       \
| nmrPipe  -fn EXT -left -sw                   \
| nmrPipe  -fn TP                                               \
| nmrPipe  -fn SP -off 0.4 -end 0.98 -pow 2 -c 0.5              \
| nmrPipe  -fn ZF -auto \
| nmrPipe  -fn FT                                               \
| nmrPipe  -fn PS -p0 0.0 -p1 0.0 -di                       \
| nmrPipe  -fn TP                                               \
| nmrPipe  -fn COADD -cList 1 0 -time -axis Y \
| nmrPipe  -fn POLY -auto \
-verb -ov -out A.ft2

I chage cList to 0 1 to get the 2nd part. Things looks OK in nmrDraw, however, there is a 2nd copy of the protein spectrum that folds from the top to the bottom of the y axis. The other copy is centered, but condensed along the y-axis. I am not sure why there are 2 copies of the spectrum appearing (besided the IP, and AP ones). The spectral widths are set up properly for this protein, and the HSQC with the same sw looks normal (1 copy). Maybe this is something to do with using -complex for processing the y dimension, where I normally use rance-kay. Any ideas? Thanks.

link

answered Mar 03 '10 at 12:38

Elio Cino
31

updated Mar 03 '10 at 13:02

Evgeny Fadeev
577●1

interesting. I've updated this http://qa.nmrwiki.org/question/33/how-to-process-gnhsqc_ipapc-data-with-nmrpipe#35 with the complete conversion script - Evgeny Fadeev (Mar 03 '10 at 13:14)

just checked the gNhsqc_IPAP.c sequence. It is not using rance/kay (echo-antiecho) method. Please correct me if I am wrong. - Evgeny Fadeev (Mar 03 '10 at 13:19)

why don't you try removing -axis Y? - Evgeny Fadeev (Mar 03 '10 at 14:16)

I removed the -axis Y, but the spectrum looks the same (2 copies showing up). No idea why... - Elio Cino (Mar 04 '10 at 05:06)

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