poky tutorial

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From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Wednesday, July 7, 2021 at 2:47 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] poky tutorial

[External Email - Use Caution]

Is there a place where I can learn poky? The help documents on poky are most for sparky or nmrfam-sparky. What I'm interested now is how to prepare the data for NOE assignment and structural calculation. While there is nothing about the former issue, there is only youtube video on preparation for structural calculation but it goes at super expert level and I don't get much as a beginner user. A detailed documentation about these procedures will definitely benefit newcomers and help spreading the wonderful suite to the structural biology community.

Thanks.

Jun

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Jun Yang

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Jul 7, 2021, 7:14:26 PM7/7/21

to NMR POKY/SPARKY USER GROUP

Thanks for the information. In my understanding, PONDEROSA-C/S are for structural calculation, right? What about NOE assignment? I don't need to install Ponderosa Client and Ponderosa Analyzer if I have Poky suite, right?

Lee, Woonghee

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Jul 7, 2021, 7:16:53 PM7/7/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

NOE assignment is concurrently conducted with structure calculation. Check this paper out: https://link.springer.com/article/10.1007/s10858-016-0036-y

POKY includes all necessities and you don’t need to install PONDEROSA-C/S separately.

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

Shipping/Mailing Address:

Woonghee Lee

1201 5^th 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 7, 2021 at 5:14 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>

Subject: Re: [NMR POKY/SPARKY] poky tutorial

[External Email - Use Caution]Thanks for the information. In my understanding, PONDEROSA-C/S are for structural calculation, right? What about NOE assignment? I don't need to install Ponderosa Client and Ponderosa Analyzer if I have Poky suite, right?

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/a5590572-4063-4b00-aeaf-3b768c16980en%40googlegroups.com.

Jun Yang

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Jul 8, 2021, 5:09:24 PM7/8/21

to NMR POKY/SPARKY USER GROUP

My test protein is about 90% backbone assigned and many of the assigned residues have sidechain assigned as well in PIPP shift table. I have the 2D 15N-HSQC spectrum with the 15N shifts are converted to pseudo-C shifts to match that in the NC-NOESY, and un-assigned 3D NC-NOESY spectrum where 15N and 13C are in the same dimension, and 13C sw is reduced so that all shifts above 48.5ppm are folded (ie, observed shift + 43ppm = real shift). With these data, do you think I can try the NOE auto assignment and structural calculation?

If so, I have following questions:

0. The first residue index of my protein doesn't start from 1, is that ok?

1. I need to convert the PIPP shift table to a format that poky accept it, ie, the resonance list? If you don't have a converter for this kind of shift table format, I can write a script for it. However, how to name the atoms for the pseudo-atom when only one atom location is visible for a methylene proton? Do I use "Q" to replace them? I see methyl protons are already named with "#" at the end so "M" may not necessary. The other issue is that I see all my N atoms are assigned as 13C in "Nuc" probably due to the shifts falling into usual 13C shift range after N-to-C conversion, I should correct them, right?

2. Because my N shifts are converted to pseudo-C shifts and many non-G Calpha are folded to a lower shifts, will these cause trouble in the "resonance outlier" checkup procedure?

3. In the "Builder" window, I can load the converted shift file other than the opened one generated by the assigned 2D spectrum, right?

4. In the additional constrain list, I see there is an option of "atomic coordinate .pdb", is this the template pdb file it refers to?

5. how to fill in the "S-S" or "cis Pro" box, do I just put like "140-150" to indicate there is a cys-cys bridge forming between residue 140 and 150, and "223" to indicate residue 223 is cis pro? If there are more than one occurrence, I can just separate them by a blank, right?

6. In my case, should I check "PACSY boost" option?

Thanks.

Jun

Lee, Woonghee

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Jul 8, 2021, 5:21:00 PM7/8/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

0. The first residue index of my protein doesn't start from 1, is that ok?

That is OK if the numbers are larger than zero and smaller than 1000.

1. I need to convert the PIPP shift table to a format that poky accept it, ie, the resonance list? If you don't have a converter for this kind of shift table format, I can write a script for it. However, how to name the atoms for the pseudo-atom when only one atom location is visible for a methylene proton? Do I use "Q" to replace them? I see methyl protons are already named with "#" at the end so "M" may not necessary. The other issue is that I see all my N atoms are assigned as 13C in "Nuc" probably due to the shifts falling into usual 13C shift range after N-to-C conversion, I should correct them, right?

I wrote PIPP shift table support five years ago but haven’t tested much. But the nomenclature needs to be dealt with. You can simply detach #. You can use Q or M for your bookkeeping but it isn’t necessary to run program.

2. Because my N shifts are converted to pseudo-C shifts and many non-G Calpha are folded to a lower shifts, will these cause trouble in the "resonance outlier" checkup procedure?

They should have corrected (aliased) chemical shifts.

3. In the "Builder" window, I can load the converted shift file other than the opened one generated by the assigned 2D spectrum, right?

You can do both. You are referring the difference between “Import” button and “Open” button.

4. In the additional constrain list, I see there is an option of "atomic coordinate .pdb", is this the template pdb file it refers to?

If your calculation option is related to automated NOE assignment, that will work as decoys (initial structure is a stretched thread). If not (constraint only), the pdb will be the initial structure and you are refining the structure from there.

5. how to fill in the "S-S" or "cis Pro" box, do I just put like "140-150" to indicate there is a cys-cys bridge forming between residue 140 and 150, and "223" to indicate residue 223 is cis pro? If there are more than one occurrence, I can just separate them by a blank, right?

Use comma to separate. If you place your cursor in the box for a few seconds, it just shows the hint.

6. In my case, should I check "PACSY boost" option?

You can submit two different jobs and see what gives better results.

Cheers,

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

https://bmrb.io/software/starch/filesel.php?tagcat=Atom_chem_shift

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

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From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Thursday, July 8, 2021 at 3:09 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky tutorial

[External Email - Use Caution]My test protein is about 90% backbone assigned and many of the assigned residues have sidechain assigned as well in PIPP shift table. I have the 2D 15N-HSQC spectrum with the 15N shifts are converted to pseudo-C shifts to match that in the NC-NOESY, and un-assigned 3D NC-NOESY spectrum where 15N and 13C are in the same dimension, and 13C sw is reduced so that all shifts above 48.5ppm are folded (ie, observed shift + 43ppm = real shift). With these data, do you think I can try the NOE auto assignment and structural calculation?

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/15144610-8613-4d75-b106-687d482a51b7n%40googlegroups.com.

Gabriel Cornilescu

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Jul 8, 2021, 7:12:24 PM7/8/21

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On 7/8/21 5:20 PM, Lee, Woonghee wrote:

Hi Jun,

0. The first residue index of my protein doesn't start from 1, is that ok?

That is OK if the numbers are larger than zero and smaller than 1000.

1. I need to convert the PIPP shift table to a format that poky accept it, ie, the resonance list? If you don't have a converter for this kind of shift table format, I can write a script for it. However, how to name the atoms for the pseudo-atom when only one atom location is visible for a methylene proton? Do I use "Q" to replace them? I see methyl protons are already named with "#" at the end so "M" may not necessary. The other issue is that I see all my N atoms are assigned as 13C in "Nuc" probably due to the shifts falling into usual 13C shift range after N-to-C conversion, I should correct them, right?

I wrote PIPP shift table support five years ago but haven’t tested much. But the nomenclature needs to be dealt with. You can simply detach #. You can use Q or M for your bookkeeping but it isn’t necessary to run program.

https://bmrb.io/software/starch/help/pipp.shtml

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/58309151-AC9A-48F2-989C-2715BC514566%40ucdenver.edu.

Jun Yang

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Jul 8, 2021, 9:06:42 PM7/8/21

to NMR POKY/SPARKY USER GROUP

Hi Woonghee,

Thanks for the prompt reply. I need a bit more clarification on some questions:

On Thursday, July 8, 2021 at 5:21:00 PM UTC-4 Lee, Woonghee wrote:

Hi Jun,

1. I need to convert the PIPP shift table to a format that poky accept it, ie, the resonance list? If you don't have a converter for this kind of shift table format, I can write a script for it. However, how to name the atoms for the pseudo-atom when only one atom location is visible for a methylene proton? Do I use "Q" to replace them? I see methyl protons are already named with "#" at the end so "M" may not necessary. The other issue is that I see all my N atoms are assigned as 13C in "Nuc" probably due to the shifts falling into usual 13C shift range after N-to-C conversion, I should correct them, right?

I wrote PIPP shift table support five years ago but haven’t tested much. But the nomenclature needs to be dealt with. You can simply detach #. You can use Q or M for your bookkeeping but it isn’t necessary to run program.

I'm a bit confused. Should I NOT use "Q" or "M" in the resonance list file? If so, how to name the methlyene proton if I only observe one shift, use HB# as in xplor-nih to represent either HB1 or HB2 or both, since this form can then be directly exported to xplor-nih constrains? What about the wrong nucleus assignment for 15N, I need to correct that during the format conversion, right?

2. Because my N shifts are converted to pseudo-C shifts and many non-G Calpha are folded to a lower shifts, will these cause trouble in the "resonance outlier" checkup procedure?

They should have corrected (aliased) chemical shifts.

Do you mean I need to correct them to the corresponding normal values? I thought this shift table will be used to assign the NOEs. If these shifts are correctly back to normal 15N shifts and Ca shifts, they will not be found in the spectra, isn't that an issue?

4. In the additional constrain list, I see there is an option of "atomic coordinate .pdb", is this the template pdb file it refers to?

If your calculation option is related to automated NOE assignment, that will work as decoys (initial structure is a stretched thread). If not (constraint only), the pdb will be the initial structure and you are refining the structure from there.

The first job I send will be for automated NOE assignment, then I don't need to provide any pdb file, right? Will the NOE assignment help to identify more unassigned atoms? What result do I expect after this job is done, NOE assignment only or with initial structure calculation result as well?

Thanks a lot.

Jun

Lee, Woonghee

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Jul 8, 2021, 9:14:14 PM7/8/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

I’m a bit confused. Should I NOT use “Q” or “M” in the resonance list file? If so, how to name the ethylene proton if I only observe one shift, use HB# as in xplor-nih to represent either HB1 or HB2 or both, since this form can then be directly exported to xplor-nih constrains? What about the wrong nucleus assignment for 15N, I need to correct that during the format conversion, right?

You should change it to HB or QB.

Do you mean I need to correct them to the corresponding normal values? I thought this shift table will be used to assign the NOEs. If these shifts are correctly back to normal 15N shifts and Ca shifts, they will not be found in the spectra, isn't that an issue?

They need to be in normal range. Both your chemical shifts in the resonance table and peak and in the noesy peak list. In the case of ambiguous NOE peak that can be assigned to multiple resonances, chemical shift distribution plays a role in calculating probabilities.

The first job I send will be for automated NOE assignment, then I don't need to provide any pdb file, right? Will the NOE assignment help to identify more unassigned atoms? What result do I expect after this job is done, NOE assignment only or with initial structure calculation result as well?

Yes if you stick with constraint only options after the initial run. If you want to collect more constraints, you may use intermediate structures. You can just try a few different combinations and you will understand how they differ.

Cheers,

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/0abfc79b-9eb3-4229-9aa5-0c8ebd8ac1e9n%40googlegroups.com.

Jun Yang

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Jul 8, 2021, 9:53:12 PM7/8/21

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On Thursday, July 8, 2021 at 9:14:14 PM UTC-4 Lee, Woonghee wrote:

Hi Jun,

I’m a bit confused. Should I NOT use “Q” or “M” in the resonance list file? If so, how to name the ethylene proton if I only observe one shift, use HB# as in xplor-nih to represent either HB1 or HB2 or both, since this form can then be directly exported to xplor-nih constrains? What about the wrong nucleus assignment for 15N, I need to correct that during the format conversion, right?

You should change it to HB or QB.

So for the single methylene shift, I can name it as HB or QB; for Ala methyl, I can name it as HB# or MB; what about the two degenerated methyls in Leu or Val, do I name it as QMD/QMG?

Do you mean I need to correct them to the corresponding normal values? I thought this shift table will be used to assign the NOEs. If these shifts are correctly back to normal 15N shifts and Ca shifts, they will not be found in the spectra, isn't that an issue?

They need to be in normal range. Both your chemical shifts in the resonance table and peak and in the noesy peak list. In the case of ambiguous NOE peak that can be assigned to multiple resonances, chemical shift distribution plays a role in calculating probabilities.

I think I need to describe my data better. For example, one N shift normally is 120ppm, and one Ca shift normally is 58ppm, in my nc-noesy spectrum, that particular N shift will be converted to pseudo-C and becomes at 24ppm, and the particular Ca shift will be folded to 15ppm because my spectral window is set at 5.5-48.5ppm. So in this case, if I correct the N and Ca shifts back to their normal range of 120ppm and 58ppm, will the program find the plane of that N and Ca at 24ppm and 15ppm, respectively?

Lee, Woonghee

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Jul 8, 2021, 9:58:26 PM7/8/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

Use HB or MB for A and HD/HG for L/V.

Again, use corrected chemical shifts both in the resonance list and the peak list. N should be around ~120 and CA ~58.

Woonghee

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Sent: Thursday, July 8, 2021 7:53 PM

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Jun Yang

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Jul 26, 2021, 8:21:46 PM7/26/21

to NMR POKY/SPARKY USER GROUP

Hi Woonghee,

After intensive work of data cleanup, I finally collected all the shifts I have for NC-NOESY assignment. There is no atom name violation and shift derivations are less than 0.2ppm for C/N and 0.02ppm for H. So right now, all the chemical shifts are within the typical ranges of their types. However, as I mentioned earlier, in my NC-NOESY dataset, N shift needs to be converted to pseduo-C shift and non-Gly Ca and ST Cb needs to fold back in order to find their proper Z plane. Where should I provide such information in poky?

Bests

Jun

Lee, Woonghee

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Jul 26, 2021, 11:15:46 PM7/26/21

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--

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

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Date: Monday, July 26, 2021 at 9:14 PM
To: Jun Yang <yangj...@gmail.com>
Subject: Re: [NMR POKY/SPARKY] poky tutorial

Hi Jun,

Do you mean your chemical shifts on spectra are not converted by aliasing? Or, you mean NOESY data need conversion? There’s no need to put that information somewhere. You can just apply aliases to the peaks need them.

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/eba720f0-3ec5-4b00-ad27-f29a802295ecn%40googlegroups.com.

Jun Yang

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Jul 26, 2021, 11:57:24 PM7/26/21

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Hi Woonghee,

I think I need to describe my data better. For example, I have one N shift at 120ppm in regular N-HSQC, and I have one Ca shift at 58ppm in regular C-HSQC. In my nc-noesy spectrum, that particular N shift need be converted to pseudo-C according to formula [Ccenter + (Nshift - Ncenter) x Csw / Nsw] and becomes at 24ppm, and the particular Ca shift will be folded to 15ppm because my spectral window is set at 5.5-48.5ppm (see the attached 2D projection of the NC-NOESY data, the negative peaks on the left half are converted amide protons and the peaks on the top middle are are folded H/Calpha).

Right now in my resonance list, these two atoms are at 120ppm and 58ppm as you suggested in early email. These normal shifts need to be converted in order to match the NC-NOESY dataset. My question is whether I need to also provide the converted shifts for the NC-NOESY data.

Thanks.

Jun

o_H-acq.C.dat_9x7.png

Lee, Woonghee

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Jul 27, 2021, 1:08:03 AM7/27/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

You have to convert the noesy data not the shift table to make them compatible to the noesy data. I think I have mentioned that. After picking noe peaks, the chemical shifts of the noe peaks need to be corrected. That is preferred because chemical shifts matter in the noe assignment.

Woonghee

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Sent: Monday, July 26, 2021 9:57:23 PM

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Subject: Re: FW: [NMR POKY/SPARKY] poky tutorial

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Jun Yang

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Jul 27, 2021, 9:31:30 AM7/27/21

to Lee, Woonghee, NMR POKY/SPARKY USER GROUP

You mean to re-process the data so that the shifts in the new data match the normal shift ranges of corresponding atom types?

If so, I guess I can process the C dimension as N, which would take care of N shifts, but how to alias those Calpha without modifying the rest carbon shifts?

Jun

Gabriel Cornilescu

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Jul 27, 2021, 11:34:19 AM7/27/21

to Jun Yang, Lee, Woonghee, NMR POKY/SPARKY USER GROUP

You could use CS (circular shift) and EXT (extract) functions of NMRPipe and extract two unaliased regions of the spectra seprately (as two spectra)...

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Lee, Woonghee

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Jul 27, 2021, 12:08:28 PM7/27/21

to Gabriel Cornilescu, Jun Yang, NMR POKY/SPARKY USER GROUP

I second that.

--

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

https://groups.io/g/nmrpipe

Shipping/Mailing Address:

Woonghee Lee

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Jun Yang

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Jul 27, 2021, 12:40:40 PM7/27/21

to NMR POKY/SPARKY USER GROUP

So basically you suggest that I convert the nc-noesy dataset into three datasets: one has N shifts, one has correct Calpha shifts via CS but all other carbons shifts are wrong, and the third one will be the original dataset with all other carbon shifts correct but Calpha shift wrong, right?

What do I need EXT function for, to extract proton regions only belong to amide protons in "n-noesy" and only belong to aliphatic protons in the other two "c-noesy"? If so, I think that's unnecessary because without extraction, there is directly symmetry in the SAME dataset, otherwise, it needs to search for symmetry in different datasets, right?

Thanks again for all the help.

Jun

Lee, Woonghee

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Jul 27, 2021, 12:53:02 PM7/27/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

I think you can still keep one spectrum for C. But that is an nmrpipe question.

Meanwhile, I will think about the nmrglue method that you can run on poky.

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

Shipping/Mailing Address:

Woonghee Lee

1201 5^th 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: Tuesday, July 27, 2021 at 10:41 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky tutorial

[External Email - Use Caution]So basically you suggest that I convert the nc-noesy dataset into three datasets: one has N shifts, one has correct Calpha shifts via CS but all other carbons shifts are wrong, and the third one will be the original dataset with all other carbon shifts correct but Calpha shift wrong, right?

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/031bbcd2-44c4-4690-bb89-4186198214bbn%40googlegroups.com.

Jun Yang

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Jul 27, 2021, 1:21:36 PM7/27/21

to NMR POKY/SPARKY USER GROUP

Hi Woonghee,

Can you give me direct instructions of how to prepare my data for the server, ie, dataset conversion and extraction like I mentioned in previous email?

Thanks.

Jun

Gabriel Cornilescu

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Jul 27, 2021, 1:28:46 PM7/27/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

The purpose of the EXT would be to remove any aliased spectral region and provide the automated assignment algorithm with (complementary) spectral regions that have the correct chemical shifts in ALL dimensions. I am not sure if the algorithm uses the NOESY symmetry.

---
Gabriel Cornilescu
cornilescu.org

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Lee, Woonghee

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Jul 27, 2021, 1:30:44 PM7/27/21

to yangj...@gmail.com, NMR POKY/SPARKY USER GROUP

Dear Jun,

What server? There are multiple servers associated with Poky. You mean structure calculation? Then, see below:

Click this button in the Poky main window.

From the Poky Structure Builder window:

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