draw 1D slice along Z axis in a 3D dataset

118 views
Skip to first unread message

Jun Yang

unread,
Jul 22, 2021, 11:00:42 AM7/22/21
to NMR POKY/SPARKY USER GROUP
Hi Colleagues,

In Sparky, we can use "vS" to draw 1D slice along X/Y axis in a 3D dataset. Is there a function to do the same thing along Z axis?

Thanks in advance.

Jun

Lee, Woonghee

unread,
Jul 22, 2021, 11:40:58 AM7/22/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

You can just rotate the cube by “xr”. Do you expect to see something different?

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Thursday, July 22, 2021 at 9:01 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]Hi Colleagues,

 

In Sparky, we can use "vS" to draw 1D slice along X/Y axis in a 3D dataset. Is there a function to do the same thing along Z axis?

 

Thanks in advance.

 

Jun

--
You received this message because you are subscribed to the Google Groups "NMR POKY/SPARKY USER GROUP" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nmr-sparky+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/a3411e85-5de7-4ae6-a5d2-8b9125e3551cn%40googlegroups.com.

Jun Yang

unread,
Jul 22, 2021, 12:27:25 PM7/22/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

Thanks. The "xr" command works ok for my purpose to see whether the peak of interest is also at top along Z axis, I just need to first make the peak to the center of spectrum. However, I see this function only apply to the dataset where the peak locates. I don't know how difficult to implement this change, but I think it would be better to have it apply to all dataset that are synchronized in all three dimensions. For example, in synchronized HNCACO and HNCO, I found the center of a peak locations is different in HNCACO vs HNCO, meaning there is degeneracy of an inter-CO and an intra-CO. When I use "xr" on one spectrum, I have to run "xr" on the other one and make sure they are displayed in the same order of three axes. If "xr" works on both spectra since they are synchronized, it would be a lot easier to see without the worry that wrong axes order are chosen.

Another thing is about region definition and application. In both Sparky and NMRFAM-Sparky, "rt" is used to bring up the region table to define spectrum regions and assign accelerator, eg, I use "na" to define an "amide proton - aliphatic proton" region. However, in Sparky I can run a command "rgna" to set the current spectrum to the desired "amide-aliphatic" region, but in NMRFAM-Sparky, "go to region X" with the shortcut "rgX" also brings up the region table, ie, it works the same as "rt". Also if I type "rgX", the "Group dialog" window pops up as the command "rg", and I don't think it has anything to do with region application. This gives me the impression that in NMRFAM-Sparky, the shortcut for "go to region X" doesn't work anymore. I can only apply through region table, it, open region table, select the pre-defined region and then click "Goto" to apply it, is that right?

Bests,

Jun

Lee, Woonghee

unread,
Jul 22, 2021, 12:33:12 PM7/22/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

I recommend using “vd” to make secondary views matching with your dimension interests and synchronizing them together. That will work.

 

However, in Sparky I can run a command "rgna" to set the current spectrum to the desired "amide-aliphatic" region, but in NMRFAM-Sparky, "go to region X" with the shortcut "rgX" also brings up the region table, ie, it works the same as "rt". Also if I type "rgX", the "Group dialog" window pops up as the command "rg", and I don't think it has anything to do with region application. This gives me the impression that in NMRFAM-Sparky, the shortcut for "go to region X" doesn't work anymore. I can only apply through region table, it, open region table, select the pre-defined region and then click "Goto" to apply it, is that right?

 

That probably is. That will be fixed in poky soon.

 

Best,

Woonghee

 

 

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>


Date: Thursday, July 22, 2021 at 10:27 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>

Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]Hi Woonghee,

Lee, Woonghee

unread,
Jul 27, 2021, 4:30:43 PM7/27/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Another thing is about region definition and application. In both Sparky and NMRFAM-Sparky, "rt" is used to bring up the region table to define spectrum regions and assign accelerator, eg, I use "na" to define an "amide proton - aliphatic proton" region. However, in Sparky I can run a command "rgna" to set the current spectrum to the desired "amide-aliphatic" region, but in NMRFAM-Sparky, "go to region X" with the shortcut "rgX" also brings up the region table, ie, it works the same as "rt". Also if I type "rgX", the "Group dialog" window pops up as the command "rg", and I don't think it has anything to do with region application. This gives me the impression that in NMRFAM-Sparky, the shortcut for "go to region X" doesn't work anymore. I can only apply through region table, it, open region table, select the pre-defined region and then click "Goto" to apply it, is that right?

 

 

Best,

Woonghee

 

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>


Date: Thursday, July 22, 2021 at 10:27 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>

Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]Hi Woonghee,

Jun Yang

unread,
Jul 28, 2021, 3:22:36 PM7/28/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

Thanks for the effort. It works smoothly.

Here is another feature to be considered. In sparky, when I minimize the main sparky window, all opened windows related to sparky will also be minimized, which is quite nice considering how many windows can be opened in sparky. However, this feature is no longer in poky, ie, minimizing poky window only minimizes that one window and all other windows remain open. Is there an equivalent function to minimize all opened windows to clear up the space for other task temporarily?

As Gabriel suggested about extracting region of 3D dataset so that all diagonal peaks will be unaliased. However, in my data, it's quite difficult to cut regions without any aliased peaks since they are intertwined unless I choose very small regions that include only a few peaks, then I'll end up with many datasets. How restrict is the requirement to have no aliased peak? Is it possible to have a small amount aliased peaks in the dataset?

Bests,

Jun

Lee, Woonghee

unread,
Jul 28, 2021, 5:05:15 PM7/28/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

Here is another feature to be considered. In sparky, when I minimize the main sparky window, all opened windows related to sparky will also be minimized, which is quite nice considering how many windows can be opened in sparky. However, this feature is no longer in poky, ie, minimizing poky window only minimizes that one window and all other windows remain open. Is there an equivalent function to minimize all opened windows to clear up the space for other task temporarily?

 

 

You can click hide button (red eye) when you are selecting the particular molecule.

 

As Gabriel suggested about extracting region of 3D dataset so that all diagonal peaks will be unaliased. However, in my data, it's quite difficult to cut regions without any aliased peaks since they are intertwined unless I choose very small regions that include only a few peaks, then I'll end up with many datasets. How restrict is the requirement to have no aliased peak? Is it possible to have a small amount aliased peaks in the dataset?

 

 

Just select some peaks and apply Alias to them.

Jun Yang

unread,
Jul 28, 2021, 5:27:19 PM7/28/21
to NMR POKY/SPARKY USER GROUP
I think you mis-understood my questions, see below under your comments. Thanks.     Jun

On Wednesday, July 28, 2021 at 5:05:15 PM UTC-4 Lee, Woonghee wrote:

Hi Jun,

 

Here is another feature to be considered. In sparky, when I minimize the main sparky window, all opened windows related to sparky will also be minimized, which is quite nice considering how many windows can be opened in sparky. However, this feature is no longer in poky, ie, minimizing poky window only minimizes that one window and all other windows remain open. Is there an equivalent function to minimize all opened windows to clear up the space for other task temporarily?

 

 

You can click hide button (red eye) when you are selecting the particular molecule.

I'm not talking about one particular window, but all windows that are opened with poky. In sparky, if I minimize the main sparky window, it minimizes all opened windows. That's a feature that I would like to see in poky. 

 

As Gabriel suggested about extracting region of 3D dataset so that all diagonal peaks will be unaliased. However, in my data, it's quite difficult to cut regions without any aliased peaks since they are intertwined unless I choose very small regions that include only a few peaks, then I'll end up with many datasets. How restrict is the requirement to have no aliased peak? Is it possible to have a small amount aliased peaks in the dataset?

 

 

Just select some peaks and apply Alias to them.

Aliasing these folded c-alpha peaks will set the shifts correctly, but the actual data doesn't change, right? I thought you want me to adjust the dataset itself so that the peaks locate at their proper position. That's why Gabriel suggest the CS and EXT function in nmrpipe to create subset of data containing the unbiased peaks. My question is that in each of these subset data, is it possible that it still have a small number of aliased peaks because they are intertwined? For example, some Thr beta H/C is close to some HY beta H/C duo to folding. 

Lee, Woonghee

unread,
Jul 28, 2021, 5:31:38 PM7/28/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

  1. All the view windows defined as one molecule will be affected by your clicks. Let say if you have 10 spectra “undefined” which is default, they all hide/show when you click that hide/show button if you are selecting “(undefined molecule)”.
  2. Actual data doesn’t change. You can apply the alias to only selected peak. Regardless of their closeness, you can selectively alias one peak and unalias another.

 

Best,

Woonghee

 

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Wednesday, July 28, 2021 at 3:27 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]I think you mis-understood my questions, see below under your comments. Thanks.     Jun

Jun Yang

unread,
Jul 28, 2021, 5:46:56 PM7/28/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

Thanks for the clarification of issue 1. 

In regarding issue 2, I do need to convert the actual data to have unaliased peak locations along H-acquisition axis and C axis, right?

Lee, Woonghee

unread,
Jul 28, 2021, 5:53:26 PM7/28/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

Your issue 2 question is unclear. Your data is true to majority of peaks, you can only use alias tools for the folded peaks while you don’t do anything for the unfolded peaks. What further conversion are you asking? Once you follow Gabriel’s suggestion, that’s all good, right?

 

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Wednesday, July 28, 2021 at 3:47 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]Hi Woonghee,

 

Thanks for the clarification of issue 1. 

Image removed by sender.

 

You can click hide button (red eye) when you are selecting the particular molecule.

I'm not talking about one particular window, but all windows that are opened with poky. In sparky, if I minimize the main sparky window, it minimizes all opened windows. That's a feature that I would like to see in poky. 

 

As Gabriel suggested about extracting region of 3D dataset so that all diagonal peaks will be unaliased. However, in my data, it's quite difficult to cut regions without any aliased peaks since they are intertwined unless I choose very small regions that include only a few peaks, then I'll end up with many datasets. How restrict is the requirement to have no aliased peak? Is it possible to have a small amount aliased peaks in the dataset?

 

Image removed by sender.

Jun Yang

unread,
Jul 28, 2021, 5:55:25 PM7/28/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

Is it possible to call you at your office when you are available? Sometime I feel the email communication is not very efficient.

Bests,

Jun

Jun Yang

unread,
Jul 29, 2021, 6:22:55 PM7/29/21
to NMR POKY/SPARKY USER GROUP
In the structure builder window, when I clip the 1st icon in the "NMR thru space data" section and choose the opened c-noesy (the aliphatic region of the nc-noesy with the Calpha peaks unaliazed) and n-noesy (the amide region of the nc-noesy with N shift corrected), it pops out error message saying that "the file is invalid". Is that because I didn't no assignments in them? Since my main test goal is for auto NOE assignment, what should I do?

Also when I input the protein sequence, it automatically index it from 1. Do I need to change it manually to the value I prefer so that it matches the chemical shifts?

Thanks.

Jun

Lee, Woonghee

unread,
Jul 29, 2021, 6:27:31 PM7/29/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
Hi Jun,

Do you have peaks picked? PSB uses peak positions to find the experiment type. If you are opening a file not importing, you should use correct file extensions (e.g. .list) not something you use differently.

If your sequence file is three letter .seq file, it uses index number in the second column. But your chemical shift file should agree with that.

Best,
Woonghee
From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Sent: Thursday, July 29, 2021 4:22:55 PM

To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset
 
[External Email - Use Caution]In the structure builder window, when I clip the 1st icon in the "NMR thru space data" section and choose the opened c-noesy (the aliphatic region of the nc-noesy with the Calpha peaks unaliazed) and n-noesy (the amide region of the nc-noesy with N shift corrected), it pops out error message saying that "the file is invalid". Is that because I didn't no assignments in them? Since my main test goal is for auto NOE assignment, what should I do?

Jun Yang

unread,
Jul 30, 2021, 12:02:20 AM7/30/21
to NMR POKY/SPARKY USER GROUP
So I only need to pick the peaks and don't need to assign them, right? As for the three letter .seq file, do you have a template that I can follow, like this?

gly 124
ala 125
...

Thanks.

Jun

Lee, Woonghee

unread,
Jul 30, 2021, 10:15:31 AM7/30/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Dear Jun,

 

Don’t expect the automation is 100% perfect. If you have some manually assigned peaks, it will help the automation greatly. Picked peaks’ position must be correct not folded. You now know how to make them aliased.

 

For the file format, you can open the poky notepad and “File -> File Formats” is where you can find.

 

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Thursday, July 29, 2021 at 10:02 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]So I only need to pick the peaks and don't need to assign them, right? As for the three letter .seq file, do you have a template that I can follow, like this?

Image removed by sender.

 

You can click hide button (red eye) when you are selecting the particular molecule.

I'm not talking about one particular window, but all windows that are opened with poky. In sparky, if I minimize the main sparky window, it minimizes all opened windows. That's a feature that I would like to see in poky. 

 

As Gabriel suggested about extracting region of 3D dataset so that all diagonal peaks will be unaliased. However, in my data, it's quite difficult to cut regions without any aliased peaks since they are intertwined unless I choose very small regions that include only a few peaks, then I'll end up with many datasets. How restrict is the requirement to have no aliased peak? Is it possible to have a small amount aliased peaks in the dataset?

 

Image removed by sender.

Jun Yang

unread,
Jul 30, 2021, 1:06:33 PM7/30/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

I see. It gives me the impression that the program does NOT look at the real data, ONLY the peak shift list files generated by the data, is that right?

Thanks.

Jun

Jun Yang

unread,
Jul 30, 2021, 4:00:25 PM7/30/21
to NMR POKY/SPARKY USER GROUP
Hi Wonnghee,

I have some questions about the APES peak picking.

1. it asks for protein sequence. I think the purpose of that is to calculation how many residues in total. How does this data affect the peak picking? 
2. when I try to pick peaks base on c-hsqc in c-noesy dataset, why it also asks for n-hsqc data?
3. what does the "Filter" button use for, it doesn't seem to do anything?
4. is there a way to limit peak picking from other selected peaks in 2D spectrum as that in "kr"?

Thanks.

Jun

Lee, Woonghee

unread,
Aug 1, 2021, 9:39:49 AM8/1/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

You’re correct.

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Friday, July 30, 2021 at 11:06 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]Hi Woonghee,

 

I see. It gives me the impression that the program does NOT look at the real data, ONLY the peak shift list files generated by the data, is that right?

 

Thanks.

 

Jun

On Friday, July 30, 2021 at 10:15:31 AM UTC-4 Lee, Woonghee wrote:

Dear Jun,

 

Don’t expect the automation is 100% perfect. If you have some manually assigned peaks, it will help the automation greatly. Picked peaks’ position must be correct not folded. You now know how to make them aliased.

 

For the file format, you can open the poky notepad and “File -> File Formats” is where you can find.

 

Image removed by sender.

Error! Filename not specified.

 

You can click hide button (red eye) when you are selecting the particular molecule.

I'm not talking about one particular window, but all windows that are opened with poky. In sparky, if I minimize the main sparky window, it minimizes all opened windows. That's a feature that I would like to see in poky. 

 

As Gabriel suggested about extracting region of 3D dataset so that all diagonal peaks will be unaliased. However, in my data, it's quite difficult to cut regions without any aliased peaks since they are intertwined unless I choose very small regions that include only a few peaks, then I'll end up with many datasets. How restrict is the requirement to have no aliased peak? Is it possible to have a small amount aliased peaks in the dataset?

 

Error! Filename not specified.

Lee, Woonghee

unread,
Aug 1, 2021, 9:47:26 AM8/1/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

1. it asks for protein sequence. I think the purpose of that is to calculation how many residues in total. How does this data affect the peak picking? 

It briefly limits chemical shift ranges to look over for peak picking. But more importantly, like you say, # of peaks for the certain experiment type. It helps in determining the noise level.

 

2. when I try to pick peaks base on c-hsqc in c-noesy dataset, why it also asks for n-hsqc data?

Basically, APES was developed for regular backbone peak picking and other experiments have been added later. If you only need pick sidechains, there’s no need to use APES because cross-validation to sort out noise peaks is not really useful. You can use other alternatives like restricted peak picking (kr), iPick (iP), applying F8 mode to the region (rt)…

 

3. what does the "Filter" button use for, it doesn't seem to do anything?

When you have peaks already picked some other method and you want to cross-validate and filter peaks not supported by different experiments, you can use that button. However, while your peaks are intertwined, these methods won’t work.

 

4. is there a way to limit peak picking from other selected peaks in 2D spectrum as that in "kr"?

I don’t think so for now. You can try iPick and see supported peak counts.

 

Best,

Woonghee

 

 

 

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Friday, July 30, 2021 at 2:00 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] draw 1D slice along Z axis in a 3D dataset

 

[External Email - Use Caution]Hi Wonnghee,

 

I have some questions about the APES peak picking.

 

1. it asks for protein sequence. I think the purpose of that is to calculation how many residues in total. How does this data affect the peak picking? 

2. when I try to pick peaks base on c-hsqc in c-noesy dataset, why it also asks for n-hsqc data?

3. what does the "Filter" button use for, it doesn't seem to do anything?

4. is there a way to limit peak picking from other selected peaks in 2D spectrum as that in "kr"?


Thanks.

 

Jun

On Friday, July 30, 2021 at 1:06:33 PM UTC-4 Jun Yang wrote:

Hi Woonghee,

 

I see. It gives me the impression that the program does NOT look at the real data, ONLY the peak shift list files generated by the data, is that right?

 

Thanks.

 

Jun

On Friday, July 30, 2021 at 10:15:31 AM UTC-4 Lee, Woonghee wrote:

Dear Jun,

 

Don’t expect the automation is 100% perfect. If you have some manually assigned peaks, it will help the automation greatly. Picked peaks’ position must be correct not folded. You now know how to make them aliased.

 

For the file format, you can open the poky notepad and “File -> File Formats” is where you can find.

 

Image removed by sender.

Error! Filename not specified.

 

You can click hide button (red eye) when you are selecting the particular molecule.

I'm not talking about one particular window, but all windows that are opened with poky. In sparky, if I minimize the main sparky window, it minimizes all opened windows. That's a feature that I would like to see in poky. 

 

As Gabriel suggested about extracting region of 3D dataset so that all diagonal peaks will be unaliased. However, in my data, it's quite difficult to cut regions without any aliased peaks since they are intertwined unless I choose very small regions that include only a few peaks, then I'll end up with many datasets. How restrict is the requirement to have no aliased peak? Is it possible to have a small amount aliased peaks in the dataset?

 

Error! Filename not specified.

Reply all
Reply to author
Forward
0 new messages