Subject: Re: [nmr_sparky] Re: how generate peak list from .str file of BMRB
From: Guowei Yin
Date: Jun 26, 2015

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Woonghee,

Thank you. I watched the video, it looks great. Truly, it saves time as we dont need to create peak labels by multiple clicking and typing in AT window. 

Im wondering if this approach is helpful to resolve heavily overlapping region? Does this new version sparky also have some advantages on backbone assignment? 

Best,
Guowei



2015-06-25 18:39 GMT-04:00 Woonghee Lee woonghee791113@... [nmr_sparky] nmr_sparky@yahoogroups.com :
 


The new assignment method I suggested in NMRFAM-Sparky is reducing
significant time by adapting database statistics. And that simulation
can be more accurate with using BMRB, SHIFTX2, or any other conditions
that will refine statistics from PACSY DB.

So, let say you have C(CO)NH to assign and you just finished backbone
assignments.
Then, you can use ta to simulated assignments onto C(CO)NH.

In this case, you will have something like,

K14CG_s-L15N-L15H

in you N-H strip. chemical shifts for L15N and L15H are from your
assignment so they do not have _s tag, and K14CG will have _s
because K14CG_s is arbitrary. So, you only need to check peaks with _s
assignment. Just move a bit to the peak center and type cu will center
the peak and untag _s.

By this way, you save a lot of time because traditionally what you
needed to was,

1. pick peaks (x N peaks)
2. at to bring assignment dialog
3. Type all the sequences, numbers, atoms (x N peaks)
4. Click assign button.
5. Move to the place where you have unlabel peak.

But, by adapting this predict-and-confirm method,

1. ta and click Simulate
2. Double-click _s tag peak in the peak list
3. Confirm simulated assignment by cu.

This is much easier in strip plot.

I can assure that adapting this method will be 100 times faster than
traditional pick-and-assign method. I highly recommend watching this
video: https://www.youtube.com/watch?v=tu2VSaRF2u8

Woonghee

On Thu, 2015-06-25 at 18:28 -0400, Guowei Yin puppyg.ruc@...


[nmr_sparky] wrote:

Thank you, this us very helpful.



Btw, whats _s tag?

On Thursday, June 25, 2015, Woonghee Lee woonghee791113@...
[nmr_sparky] nmr_sparky@yahoogroups.com wrote:

Great!

Because you have already loaded chemical shifts by rl, so it
worked
fine. Probably you dont have _s tags, right?

You can type BMRB code at the bottom of ta window where you
see BMRB
and Browse button.

Cheers,
Woonghee

On Thu, 2015-06-25 at 18:15 -0400, Guowei Yin
puppyg.ruc@...
[nmr_sparky] wrote:

Yes, it just works too here, even without typing BMRB
code(dont know
where to type). I clicked simulate or transfer, both worked.

On Thursday, June 25, 2015, Woonghee Lee
woonghee791113@...
[nmr_sparky] nmr_sparky@yahoogroups.com wrote:



Honestly, my memory is faint.
In the video, I did not use sequence file at all.
Also, I just tested with any ucsf file and any BMRB code, it
works
without sequence file.

Here is what I just did,

1. Run sparky
2. Open N-HSQC ucsf file (or save file)
3. ta
4. Set spectrum and type
5. Type 6452 in BMRB (that means BMRB code 6452... You can
select a file
instead).
6. Click simulate.

It works okay. 82 peaks generated.

Let me know if does not work.

Best,
Woonghee

On Thu, 2015-06-25 at 17:44 -0400, Guowei Yin
puppyg.ruc@...
[nmr_sparky] wrote:

Thanks.Sounds like for each way I need to load the
sequence
file.


Im preparing sequence file, it requires 3-letter code
sequence
file. Could you tell which format I should use for?

2015-06-25 16:55 GMT-04:00 Woonghee Lee
woonghee791113@...
[nmr_sparky] nmr_sparky@yahoogroups.com :

I forgot mentioning direct local BMRB file selection in
that
box is
doable as well.

Woonghee

On Thu, 2015-06-25 at 16:41 -0400, Guowei Yin
puppyg.ruc@...


[nmr_sparky] wrote:

Woonghee,


Thank you. by ta, I chose type N-HSQC, then click
untage, “simulate” ,  it shows no peaks
populated.
Whats wrong
with this?




By the way it looks like at the bottom of that window we
can
directly
read BMRB file, how this gonna work?


Thank you,
Guowei

2015-06-25 15:58 GMT-04:00 Woonghee Lee
woonghee791113@...
[nmr_sparky] nmr_sparky@yahoogroups.com :

Hi Guowei,

By using two-letter-code ta in NMRFAM-Sparky, you can
simulate peaks
in the Superfast assignment dialog.
You need to detach _s (meaning the peak is simualted)
by
ut (untag)
or cu (center and untag).

Best,
Woonghee

On Thu, 2015-06-25 at 15:45 -0400, Guowei Yin
puppyg.ruc@...


[nmr_sparky] wrote:

Hi all,


The new Sparky could convert .str file (NMR-STAR v3.1)
to
Sparky
resonance list. I can load this list by command rl.
But,
to use the
assignment downloaded from BMRB, I still need to
generate
a
peak list
which I could use to create peaks in Sparky. Could you
anyone tell me
how to do it? Thank you.


Best,
Guowei