Noe assignment with AUDANA/AUDASA automation

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Jun Yang

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Sep 19, 2021, 10:57:54 AM9/19/21
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Hi Woonghee,

After examining the assignments via AUDANA/SA automation, I've changed quite a bit of them and I'll re-submit the work. I have a couple questions regarding the process:

1. Do I need to adjust noe boundary at NOE auto-assignment stage (ie, calculation with AUDANA/SA automation)?

2. Do I need to adjust the angular constrains or it will be done automatically according to the latest chemical shifts?

3. Can I use one of the calculated structure as template for the next run of calculation? If so, should I add it in the "Restrains" window list?

4. You advise to run a couple times of AUDANA/SA automation to get adequate of constrains. What's the criteria to make that decision?

5. The next step is to run several times of Constraints-only X calculations for refinement, what's the purpose of those other calculation options such as: ponderosa refinement, constrains only, xplor-nih-based calculation, (ss)ponderosa-x refinement?

Thanks in advance for your help.

Jun

Jun Yang

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Sep 19, 2021, 11:10:04 AM9/19/21
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Also because my NC-noesy data can't be used easily to update the assignments in poky, I have to examine it in my traditional way and then import the assignments back in poky. When I update the peak heights via "ph", all the diagonal peak heights were changed. As you mentioned that those heights were given a constant values. Will this be taken care of in the AUDANA/SA automation?

Thanks.

Jun

Lee, Woonghee

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Sep 19, 2021, 6:34:05 PM9/19/21
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Dear Jun,

 

Diagonal peaks are nothing to do with structure calculation in solution NMR. It does not give any constraints.

 

  1. NOE boundary adjustment can be later (constraints only-x stage).
  2. Often, angle constraint violations are caused by wrong distance constraints. I recommend validating them when you reach to the point you cannot improve any further with the distance constraint validation.
  3. You can use the calculated structure as inputs in the restraints column. But you should be very careful because it will enforce your structure being very similar to the one you are providing.
  4. It all differs. When the number does not increase anymore and your structure is fairly good already?
  5. Ponderosa refinement, constraints only under CYANA-based structure calculations were used internally at NMRFAM using CYANA for folding the structure. Other calculations use Xplor-NIH.   

 

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: Sunday, September 19, 2021 at 9:10 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

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Jun Yang

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Sep 20, 2021, 3:50:16 PM9/20/21
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Hi Woonghee,

Thanks for the information. I submitted the job again. After click "calculation", I got a message saying that the data was successfully submitted to the server and I need to check my email in a few hours. However, the poky builder has this message "Updating parameters.." at the bottom of the windows. Do I need to let it run or I can close poky builder at this stage?

Thanks.

Jun

Lee, Woonghee

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Sep 20, 2021, 3:52:46 PM9/20/21
to yangj...@gmail.com, NMR POKY/SPARKY USER GROUP

Dear Jun,

 

Just ignore that message if you have received a notification from the server.

 

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

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

 


Date: Monday, September 20, 2021 at 1:50 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>

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Jun Yang

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Sep 20, 2021, 4:59:26 PM9/20/21
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Hi Woonghee,

I just got an email saying that the job (210920_143445_009) was failed due to xplor-nih error: "error reading restraint: selection string  resid  138 and name HHD*  selects no atoms". I figured it is because I use "QMD" for the degenerated Leu methyl protons. It should be converted to HD* in xplor-nih accordingly, but somehow an extra "H" was generated. Can you look into that and may sure that atom conversion runs as expected?

Thanks.

Jun

Lee, Woonghee

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Sep 20, 2021, 5:00:24 PM9/20/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

Just use HD.

 

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: Monday, September 20, 2021 at 2:59 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]

Hi Woonghee,

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Jun Yang

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Sep 20, 2021, 5:44:24 PM9/20/21
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Do you mean to replace "QMD or QMG" with "HD or HG" for degenerated Leu or Val methyls? It's quite strange since the first run had no problem with such nomenclature.

Jun

Lee, Woonghee

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Sep 20, 2021, 5:46:03 PM9/20/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

I am uncertain but you probably used MD or QD? However, I have put them in the correction list, so they will be automatically treated from now on.

 

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: Monday, September 20, 2021 at 3:44 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Do you mean to replace "QMD or QMG" with "HD or HG" for degenerated Leu or Val methyls? It's quite strange since the first run had no problem with such nomenclature.

 

Jun

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Jun Yang

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Sep 20, 2021, 5:58:55 PM9/20/21
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According to Sparky nomenclature for degenerated protons, I use follow conventions:
HB# -> MB
HG[23] -> QG
HD[12]# -> QMD (L or V)
HH[12][12] -> QQH (R)
CE[12] -> CQE (L or V or F or Y)

Jun

Lee, Woonghee

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Sep 20, 2021, 6:02:34 PM9/20/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Dear Jun,

 

That is not Sparky nomenclature. There’s no such a thing. That looks like the Cyana nomenclature to me.

Jun Yang

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Sep 21, 2021, 3:55:08 PM9/21/21
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This atom name convention is in modules/poky/atomnames.py.    Jun

Lee, Woonghee

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Sep 21, 2021, 4:00:02 PM9/21/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

That does not refer the official nomenclature for Sparky. Some modules will use that and some won’t. Best bet is to follow IUPAC.

 

--

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: Tuesday, September 21, 2021 at 1:55 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]This atom name convention is in modules/poky/atomnames.py.    Jun

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Jun Yang

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Sep 22, 2021, 1:45:37 PM9/22/21
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I should use "CD" to replace "CQD" for the degenerated delta carbon in Leu, right?

Lee, Woonghee

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Sep 22, 2021, 2:06:39 PM9/22/21
to Jun Yang, nmr-s...@googlegroups.com

CD is preferred.

 

--

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, September 22, 2021 at 11:45 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]I should use "CD" to replace "CQD" for the degenerated delta carbon in Leu, right?

Jun Yang

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Sep 27, 2021, 12:12:58 PM9/27/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

When I examined the assignments between the one I submitted and the one that came back, I found almost one third of the assignments were excluded in the returned results. Those are most NOEs between nearby residues. Is there a specific reason why they are not included in the calculation? I checked the NOEs of these assignments against the best twenty structures and most of them are within 5A.

Bests,

Jun

Lee, Woonghee

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Sep 27, 2021, 12:45:41 PM9/27/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Dear Jun,

 

There can be different reasons but I recommend checking two things.

 

  1. See BestEvaluated/final_init.upl if they are there.
  2. Check if your chemical shifts and NOE cross peaks are well agreeing.

 

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: Monday, September 27, 2021 at 10:13 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Hi Woonghee,

 

When I examined the assignments between the one I submitted and the one that came back, I found almost one third of the assignments were excluded in the returned results. Those are most NOEs between nearby residues. Is there a specific reason why they are not included in the calculation? I checked the NOEs of these assignments against the best twenty structures and most of them are within 5A.

 

Bests,

 

Jun

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Jun Yang

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Sep 27, 2021, 1:14:54 PM9/27/21
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Hi Woonghee,

Thanks for the information. 

As for option 1, I do have the file BestEvaluated/final_init.upl, what to do about it?
As for option 2, most of the peaks match well the the chemical shifts in pokybuilder.prot.

Jun

Lee, Woonghee

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Sep 27, 2021, 1:17:03 PM9/27/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

You can open the file in the text editor and see if the restraint associated with the assignment exists there. If so, you can check the score. If not, that means your assignments are not picking up that peak due to the deviation.

 

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: Monday, September 27, 2021 at 11:15 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Hi Woonghee,

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Jun Yang

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Sep 27, 2021, 4:14:45 PM9/27/21
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I checked and found about half of them are in the final_init.upl and half of them are not. By "score", do you mean the value after "#ENDURANCE"? What does it mean? And for those who aren't in the file, what kind of deviation do you refer to so that they are excluded?

Jun

Lee, Woonghee

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Sep 27, 2021, 4:20:40 PM9/27/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

Endurance score describes a restraint how far it stays in the restraint set from the penalty in the structure calculation.

https://link.springer.com/article/10.1007/s10858-016-0036-y

 

Simply, high score means highly likely true based on some criteria, and low score is opposite. Let say your NOE is unambiguous and has only one candidate, we can say it is likely true and set it high score. On the other hand, ambiguous and many probable candidates, the score will be low.

 

About the deviation, you use “tolerance” numbers for each nucleus. If they are set too small, some peaks a little off won’t be picked and assigned.

 

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: Monday, September 27, 2021 at 2:14 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]I checked and found about half of them are in the final_init.upl and half of them are not. By "score", do you mean the value after "#ENDURANCE"? What does it mean? And for those who aren't in the file, what kind of deviation do you refer to so that they are excluded?

 

Jun

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Jun Yang

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Sep 27, 2021, 4:52:10 PM9/27/21
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Of the 905 peaks that exist in final_ini.upl, I have 462 assignments with endurance score less than ten, 398 scores less than a hundred and 45 above one hundred. What's the endurance criteria that they will be discarded? What to do about them next? 

I also examined those are not in the file, they are probably due to the small tolerance I set when I submit the job, I'll increase it next time.

Jun

Lee, Woonghee

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Sep 27, 2021, 4:57:06 PM9/27/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Dear Jun,

 

Every time the structure is calculated, it will give violations based on the resulting structure. Based on violation amount (interproton distance above written in the restraint), it will reduce the endurance score. From the repetitive cycles of calculations, if one restraint keeps violating the structure, it will become below zero and be discarded.

 

If you provide your own restraints in .upl format, they will be set very high score and won’t be discarded easy.

 

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: Monday, September 27, 2021 at 2:52 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Of the 905 peaks that exist in final_ini.upl, I have 462 assignments with endurance score less than ten, 398 scores less than a hundred and 45 above one hundred. What's the endurance criteria that they will be discarded? What to do about them next? 

 

I also examined those are not in the file, they are probably due to the small tolerance I set when I submit the job, I'll increase it next time.

 

Jun

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Jun Yang

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Sep 27, 2021, 5:04:31 PM9/27/21
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I see. Can I also include those peaks that are excluded duo to shift deviation in the upl file?   Jun

Lee, Woonghee

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Sep 27, 2021, 5:06:14 PM9/27/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Yes. But, you want to identify what the issue is and correct, too.

 

--

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: Monday, September 27, 2021 at 3:04 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]I see. Can I also include those peaks that are excluded duo to shift deviation in the upl file?   Jun

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Jun Yang

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Sep 28, 2021, 12:54:42 PM9/28/21
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Hi Woonghee,

When I provide my own restrains file, I can name it to anything.upl, right? Also do I need to provide for all the peaks or just the ones that I want to keep in the calculation? And what's a good endurance value to prevent it from removal? I checked the endurance level of peaks that were excluded but in the final_init.upl, there are about 5% of them have endurance around 100000. Should I manually set a even higher value?

Bests,

Jun

Lee, Woonghee

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Sep 28, 2021, 12:57:40 PM9/28/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi June,

 

The endurance score cannot be adjusted by you. I haven’t checked the server setting yet, but your provided restraints won’t be discarded easy. For the upl file name, you probably don’t want to use predefined names (e.g. final.upl, final_init.upl, summed.upl, etc). It will complain anyways.

 

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: Tuesday, September 28, 2021 at 10:55 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Hi Woonghee,

 

When I provide my own restrains file, I can name it to anything.upl, right? Also do I need to provide for all the peaks or just the ones that I want to keep in the calculation? And what's a good endurance value to prevent it from removal? I checked the endurance level of peaks that were excluded but in the final_init.upl, there are about 5% of them have endurance around 100000. Should I manually set a even higher value?

 

Bests,

 

Jun

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Jun Yang

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Sep 28, 2021, 1:32:51 PM9/28/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

I'm a little confused when you said "the endurance score cannot be adjusted by you".  What do I artificial set in my own .upl file?

Bests

Jun

Lee, Woonghee

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Sep 28, 2021, 2:55:26 PM9/28/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

You can just follow the DIANA format. The number is internally made and used but the number provided will be neglected. You can still provide but it won’t be used.

 

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: Tuesday, September 28, 2021 at 11:33 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Hi Woonghee,

 

I'm a little confused when you said "the endurance score cannot be adjusted by you".  What do I artificial set in my own .upl file?

 

Bests

 

Jun

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Jun Yang

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Sep 28, 2021, 3:25:46 PM9/28/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

Sorry I'm not familar with Diana because we only use xplor-nih for structure calculation. I assume the .upl file format will be like final_init.upl without the "#ENDURANCE value", right? If so, how should I set the upper limit value so that the restraints won't easily get excluded during the calculation as you suggested in early email (If you provide your own restraints in .upl format, they will be set very high score and won’t be discarded easy)?

Jun

Lee, Woonghee

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Sep 28, 2021, 3:31:28 PM9/28/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

I assume the .upl file format will be like final_init.upl without the "#ENDURANCE value", right?

 

Correct.

 

If so, how should I set the upper limit value so that the restraints won't easily get excluded during the calculation as you suggested in early email (If you provide your own restraints in .upl format, they will be set very high score and won’t be discarded easy)?

 

In the past, people used to bin to “strong”, “medium” and “weak” distances based on intensities (you can guess from the “xf” window). Well, actually you can just use the “xf” window. Other approach will be the “gd” window. “xf” for binning and “gd” for continuous calibration.

 

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: Tuesday, September 28, 2021 at 1:25 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Hi Woonghee,

 

Sorry I'm not familar with Diana because we only use xplor-nih for structure calculation. I assume the .upl file format will be like final_init.upl without the "#ENDURANCE value", right? If so, how should I set the upper limit value so that the restraints won't easily get excluded during the calculation as you suggested in early email (If you provide your own restraints in .upl format, they will be set very high score and won’t be discarded easy)?

 

Jun

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Jun Yang

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Oct 16, 2021, 1:13:26 PM10/16/21
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Hi Woonghee,

I looked at the "gd" program and have a couple questions:

1. it has an option to provide five datasets, do it mean it will generate five upl/lol/wlt sets at the same time?
2. What are the parameters of "Auto calibration", "Approx", and "UPL scaler percentage" do?
3. What's the difference between "Generate" and "Run Pondersosa Cient" actions?

If I provided my own xplor-nih restrain file, can I load it in the "Restrain" window? I didn't see the option of xplor-nih for file type at the pull-down menu. If so, do I still need to load the peak lists file in the "NMR Through space data" window?

Thanks

Jun

Lee, Woonghee

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Oct 16, 2021, 1:39:26 PM10/16/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

  1. No, it will make one set. All restraints generated from selected experiments will be included in a file. If you want them separated, you can do one at a time.
  2. Auto-calibration will try to adjust the center distance after sorting by intensity. If you provide your own number, it will use that. It is something like dref in the CYANA configuration file. After calibration, you can add extra distance on top of it. From my experience, it is better to provide 20~40% more distance on the calibrated distance when running XPLOR-NIH.
  3.  Generate will generate those files. Run Ponderosa Client button just calls the Ponderosa Client program or the Poky Structure Builder.  

 

Basically, that plugin semi-automates the “xe” plugin which does bin using user custom intensities into weak, medium, and strong buckets. If you wish to use your own XPLOR-NIH restraint file, you should convert it to DIANA format to use in Poky Structure Builder. There is a Poky Notepad script in our github repository: https://github.com/pokynmr/POKY/blob/master/User_Modules/upl_tbl_conversion_script.py Depending on complexity, it may work or not.

 

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: Saturday, October 16, 2021 at 11:13 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]

Hi Woonghee,

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Jun Yang

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Oct 16, 2021, 2:13:16 PM10/16/21
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Hi Woonghee,

Thanks for the prompt reply. I'm not family with CYANA or DIANA. We only use Xplor-NIH. Is there a concept in xplor-nih that corresponding to the distance calibration you refer to? Do you mean the derivation of the distance range we set for each restrain in the xplor-nih table, eg, a range string of 3.0 1.0 2.0 means a range of (2.0 ~ 5.0), and 20% extra expands it to (1.8 ~ 5.4)? If so, how do the three parameter values control it?

Thanks.

Jun

Jun Yang

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Oct 16, 2021, 2:32:51 PM10/16/21
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By DIANA format, do you mean like this?

  125  ALA    HA   125  ALA     H 2.8 1.0 2.0
  125  ALA    HA   125  ALA    MB 2.8 1.0 2.0
  125  ALA    MB   125  ALA     H 2.8 1.0 2.0
  125  ALA    MB   125  ALA    HA 2.8 1.0 2.0
  127  GLY    QA   127  GLY     H 2.8 1.0 2.0
  127  GLY    QA   128  SER     H 2.8 1.0 2.0
  128  SER    HA   128  SER     H 2.8 1.0 2.0
  128  SER    HA   129  PRO   HD2 2.8 1.0 2.0
  128  SER    QB   128  SER    HA 2.8 1.0 2.0

Jun

Lee, Woonghee

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Oct 16, 2021, 2:35:58 PM10/16/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
Hi Jun, 

You can find the file formats in Poky Notepad. DIANA format has upper limits in .upl and lower limits in .lol. In .tbl, you have them in one line but DIANA seperates. If you don't provide .lol but only .upl, Ponderosa Server will automatically use 1.8 for interproton lower limits. 

Woonghee

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From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Sent: Saturday, October 16, 2021 12:32 PM

To: NMR POKY/SPARKY USER GROUP
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
 
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Jun Yang

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Oct 16, 2021, 2:40:12 PM10/16/21
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Thanks. What about the first question about the distance calibration and how to set them?

Lee, Woonghee

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Oct 16, 2021, 2:44:02 PM10/16/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
No that is the "gd" plugin not Xplor-NIH that calibrates based on the intensity curve on the assigned peaks.

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Sent: Saturday, October 16, 2021 12:40:12 PM
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Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
 
[External Email - Use Caution]Thanks. What about the first question about the distance calibration and how to set them?


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Jun Yang

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Oct 16, 2021, 3:43:57 PM10/16/21
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Yes, I'm asking how to set the three parameters in "gd" plugin.   Jun

Lee, Woonghee

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Oct 16, 2021, 3:49:33 PM10/16/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
I You run a couple of times with different settings and see what you get. The three numbers you use in Xplor is like the reference distance, reduction and addition numbers, right? "gd" only gives the number of reference + addition which is essentially the DIANA format. Then, Xplor parameters will be set by "reference" "reference-1.8" "0" by Ponderosa Server. Is that what you are asking?

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Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
 
[External Email - Use Caution]Yes, I'm asking how to set the three parameters in "gd" plugin.   Jun


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Jun Yang

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Oct 16, 2021, 4:02:52 PM10/16/21
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No, I'm asking the three parameters in "gd", ie, the "Auto calibration", "Approx", and "UPL scaler percentage". How to set these three values and how it affects the reference distances used in calculation.

Lee, Woonghee

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Oct 16, 2021, 4:07:09 PM10/16/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
Hi Jun,

I am suggesting you play a few times and see how they differ. The code (upl_lol.py) is there if you are interested in looking into. I cannot answer all the questions that can be studied by users. Sorry.

Woonghee

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Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
 
[External Email - Use Caution]No, I'm asking the three parameters in "gd", ie, the "Auto calibration", "Approx", and "UPL scaler percentage". How to set these three values and how it affects the reference distances used in calculation.


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Jun Yang

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Oct 16, 2021, 4:10:41 PM10/16/21
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Thanks for the advice. Have a good day.  Jun

Jun Yang

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Oct 19, 2021, 12:36:47 PM10/19/21
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Hi Woonghee,

I looked at the upl_lol.py and generated two sets of upl/lol/wlt files with default 4.5A dref or leave it blank from the two peak lists, here are my results:

1. the one without 4.5A dref have less upper limit which is understandable due to the lack of average distance addition, however, the lower limit is still set at 4.0 for all entries. Is that normal? Aren't they suppose to be 1.8A?
2. When I submit the calculation, I accidentally submit one with only the upl file, not the upl/lol/wlt file set, the calculated structures have this order: only upl (4.5A dref) is better than upl/lol/wlt (4.5A dref), and upl/lol/wlt (no dref) is the worse. Are these results normal?
3. I also looked at your script of conversion between upl and tbl and managed to convert my own xplor-nih tbl to upl and submit the calculation, and the result is pretty good in terms of structural convergence and I feel that should be enough peak assignments. According to the instruction, next I need to "run several times of Constraints-only X until I get a reasonable result". Do do this, what is the file I need to load in poky builder, just the sequence and upl file, select "NMRFAM servers" as computing on and choose "Constraints-only X" as the calculation option? I don't need the peak list files, the chemical shifts files, and PACSY boost or tolerance setting are no longer relevant, right?
4. In the "BestEvaluated/XplorCalc" folder, I see 40 structures while final.pdb contains 20. Are the 20 from the 40 structures with the lowest total energy? I also see there are 7 "ave" structure with fit & comparison RMSD, does each individual RMSD against the average of the twenty structures? What's the difference between fit and comparison RMSD?
5. In the file "final_xplor_each_##.pdb.stats",  I can see the summery of the final 20 structures. I think I can only modify the NOE violation according to the data spectra, and all the rest will be adjust by the structure calculation, is that right? What's the criteria to deem it as good enough in terms of NOE violation, for example, only 50% or below violation are above 0.5A?

Thanks again for your help.

Jun

Jun Yang

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Oct 19, 2021, 10:39:03 PM10/19/21
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Hi Woonghee,

When I looked at the file "final_xplor_each_##.pdb.stats" and realized that somehow the methylene proton that were named as "HX3" were changed to "HX1" in "noe.tbl", however, they were still "HX3" in noe.upl or noe.lol. Does this format change desired in the calculation?

Thanks

Jun

Lee, Woonghee

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Oct 19, 2021, 10:46:01 PM10/19/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
Yes, that is because Xplor vs. IUPAC nomenclature difference. Ponderosa Server changes it internally for the Xplor-NIH calculation and bring it back to IUPAC again. 

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Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
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Jun Yang

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Oct 19, 2021, 11:08:59 PM10/19/21
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Do you mean that xplor required HX1/2 format? And the pdb output will become HX2/3 format? The conversion in your server changes HX1 to HX3 and vice versa?

In my assignment, I always assign the downfield mythylene H (higher ppm) as the lower index of two (ie, HX1 in HX1/2 format or HX2 in HX2/3 format), is this going to be an issue in the calculation?

Jun

Jun Yang

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Oct 19, 2021, 11:44:52 PM10/19/21
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And "HN" is also required in xplor, but "H" is in standard pdb?

Lee, Woonghee

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Oct 19, 2021, 11:49:09 PM10/19/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
https://bmrb.io/ref_info/atom_nom.tbl

Assigning 2 vs 3 can be done your way. When calculating structure, if they don't look correct, you can exchange later. If you restraints are not tight, they will be somewhat corrected by other forces.

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Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
 
[External Email - Use Caution]And "HN" is also required in xplor, but "H" is in standard pdb?


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Jun Yang

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Oct 20, 2021, 12:15:54 AM10/20/21
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What about DIANA .upl atom nomenclature, the same as xplor-nih or BMRB format, ie, HX2/3 & H?   Jun

Lee, Woonghee

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Oct 20, 2021, 12:49:24 AM10/20/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
It is in the Eldon's BMRB link that I have just sent.

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Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
 
[External Email - Use Caution]What about DIANA .upl atom nomenclature, the same as xplor-nih or BMRB format, ie, HX2/3 & H?   Jun


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Jun Yang

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Oct 20, 2021, 9:54:50 AM10/20/21
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Thanks for the information. It's really complicated, especially when I need to use all these different programs that all have different format requirement. If I submit the .upl format as xplor-nih format, ie, HN & HX1/2, do you think Ponderosa server will complain about it?

Lee, Woonghee

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Oct 20, 2021, 9:59:47 AM10/20/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
It will complain. But you are using only my program essentially. Other associated programs are operated internally by Ponderosa Server. If you just stick with IUPAC, there's nothing you need to worry about.

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Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation
 
[External Email - Use Caution]Thanks for the information. It's really complicated, especially when I need to use all these different programs that all have different format requirement. If I submit the .upl format as xplor-nih format, ie, HN & HX1/2, do you think Ponderosa server will complain about it?


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Jun Yang

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Oct 21, 2021, 11:39:21 AM10/21/21
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Hi Woonghee,

Somehow I couldn't find your response about the five questions I had with the three upl trials. Is it possible for you to resend the response because they are very important and I'd like to keep it for future study?

Thanks in advance.

Jun

Jun Yang

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Oct 22, 2021, 9:25:37 AM10/22/21
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Hi Woonghee,

I think I've finished the step of running "constrains-only x". Should I then run the four "final step" using the same three files as the "constrains-only x" calculation in the order listed on the calculation option pull-down menu? I only need to run once for each step, right? Is there any criteria I need to look for?

Thanks for your help to guide me to close to the finish line!

Best

Jun

Lee, Woonghee

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Oct 22, 2021, 11:57:26 AM10/22/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

Options in the final step section are two different kinds – implicit vs. explicit water refinements. (x2) indicates that will run 200 structure calculations while others are 100 structure calculations without x2. Basically, you may want to go non (x2) first to save the time then go x2 to get the final version for the deposition. Inputs are basically the same, but you can also use .pdb file of previous run to refine. You should use different name than final.pdb or finalx.pdb because it will conflict with the results.

 

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, October 22, 2021 at 7:25 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

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Hi Woonghee,

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Jun Yang

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Oct 22, 2021, 1:25:29 PM10/22/21
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Hi Woonghee,

1. to add a pdb from previous run, should I choose "XplorCalc/final_xplor_ave.pdb" or "split/final.pdb_1", also is "split/final.pdb_1" the same structure with the lowest energy of the twenty, ie, the 1st filename in "XplorCalc/final_xplor_ave.pdb" under the "sort energy" column?
2. I should run implicit first, then explicit, then implicit x2, then explicit x2, or implicit first, then implicit x2, then explicit, then explicit x2
3. I only need to run one time of each step or I need run a few time until some criteria is satified? If it's the latter, what's the criteria I need to look for?
4. will each of these four steps generate twenty final structures?

Thanks.

Jun

Woonghee Lee

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Oct 22, 2021, 3:25:50 PM10/22/21
to NMR POKY/SPARKY USER GROUP

Jun,

 

  1. Just don’t use average structure. You can just final.pdb or finalx.pdb.
  2. You can submit two at once. Implicit and explicit. Then go x2 version. You can choose better one from them.
  3. It is subjective when you want to stop. If you cannot improve any more, that may be the moment. But I prefer not to have any violations in the result email. You can use wwPDB, PSVS and MolProbity validation servers to identify residues in disallowed regions.
  4. All those options will make 20 best structures in a file.

 

Best,

Woonghee

Jun Yang

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Oct 23, 2021, 3:39:03 PM10/23/21
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Hi Woonghee,

I got the results of implicit h2o and explicit h2o calculation. The "final_xplor_each_##.pdb.stats' from implict calculation now have quite a bit noe violations above 0.5 with 60% while explicit calculation has none in that catagory. Also all the energy terms in explicit is smaller than implicit. Does it mean that I should stay with explicit results and move on to implicit h2o x2 and explicit h2o x2 since no noe relaxation is necessary?

What kind of violations do you mean when you said that "I prefer not to have any violations in the result email"?

Thanks.

Jun

Lee, Woonghee

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Oct 23, 2021, 3:43:11 PM10/23/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

Proteins behave differently. So, I cannot say much about what is better or not. For the second question, the # of violations that you will report is the thing that will see from the result email from the server. That is identical to the thing that you can see in Ponderosa Analyzer when you click on the main grid of the program and click count violations. You don’t want to have significant numbers for any categories (repulsive, angle & distance).

 

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:

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1201 5th St. UCD CHEM-194

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From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Saturday, October 23, 2021 at 1:39 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]

Hi Woonghee,

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Jun Yang

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Oct 23, 2021, 3:45:00 PM10/23/21
to NMR POKY/SPARKY USER GROUP
I'm looking at the "final_xplor_each_##.pdb.stats" from "XplorCalc" folder to make above judgment. Then I found out that there is also a "final_xplor_each_##.pdb.stats" in "h2orefine/refined/" folder of explicit calculation, but not of implicit calculation. Did I check the proper one?

Jun

Lee, Woonghee

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Oct 23, 2021, 3:48:17 PM10/23/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

For the implicit calculations, structures are calculated with water molecules. So you will see the statistics file in the BestEvaluated/XplorCalc directory. On the other hands, the explicit calculations will undergo steps. 1. Simulated annealing in the vacuum, which will generate outputs in the BestEvaluated directory. 2. Water refinement, which will generate outputs under the BestEvaluated/h2orefine.

 

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: Saturday, October 23, 2021 at 1:45 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]

I'm looking at the "final_xplor_each_##.pdb.stats" from "XplorCalc" folder to make above judgment. Then I found out that there is also a "final_xplor_each_##.pdb.stats" in "h2orefine/refined/" folder of explicit calculation, but not of implicit calculation. Did I check the proper one?

 

Jun

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Jun Yang

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Oct 23, 2021, 4:42:19 PM10/23/21
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Hi Woonghee,

Duo to my screen display, I didn't realize that there is a summary section at the bottom half of the result email. Is this report all included in the zip file I downloaded?

1. So if I want to look at the final statistics of explicit, I should look for "/BestEvaluated/h2orefine/refined/final_refined_##.pdb.stats", and for implicit, I should look for "BestEvaluated/XplorCalc/final_xplor_each_##.pdb.stats", right?

2. I need to make sure the section of [VIOLATION] has zero for all three categories, right?

3. Here is the result from implicit [VIOLATION] REPULSIVE=0, ANGLE=10, DISTANCE=41 and
     explicit [VIOLATION] REPULSIVE=8, ANGLE=6, DISTANCE=10. From violation stand of point, the explicit seems better, right? If so, how should I proceed from here, keeping relaxing noe for both implicit & explicit?

Jun

Lee, Woonghee

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Oct 23, 2021, 5:53:34 PM10/23/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Dear Jun,

 

  1. Yes.
  2. It preferred. But not always necessary.
  3. You don’t have to work implicit and explicit separately. Just stick with constraints-only-x for awhile until you don’t see many violations and go back to water refinement again.

 

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: Saturday, October 23, 2021 at 2:42 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]

Hi Woonghee,

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Jun Yang

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Oct 23, 2021, 6:31:17 PM10/23/21
to NMR POKY/SPARKY USER GROUP
To run with constrains-only-x, do I need to keep relax noe to a lower percentage and/or lower violation distance?   Jun

Lee, Woonghee

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Oct 23, 2021, 6:33:53 PM10/23/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

With that option, you get the results a lot faster. I just recommend using that option until you run slower options for saving the time. That’s not related to noe calibration or something. Just time.

 

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: Saturday, October 23, 2021 at 4:31 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]To run with constrains-only-x, do I need to keep relax noe to a lower percentage and/or lower violation distance?   Jun

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Jun Yang

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Oct 23, 2021, 6:40:37 PM10/23/21
to NMR POKY/SPARKY USER GROUP
I thought that I have to change something in order to improve the structure quality, but according to you suggestion, I can use the same upl file and just choose constraints-only-x and it will reduce the three violation parameters. So I'll keep doing that until no further improve, then I go back to the implicit & explicit calculation option. Is that right?

Jun

Lee, Woonghee

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Oct 23, 2021, 6:42:48 PM10/23/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Same upl but you will get more violations. I am suggesting refining constraints during running constraints-only-x iteratively because it is faster. Then you go the final step.

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: Saturday, October 23, 2021 at 4:40 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]

I thought that I have to change something in order to improve the structure quality, but according to you suggestion, I can use the same upl file and just choose constraints-only-x and it will reduce the three violation parameters. So I'll keep doing that until no further improve, then I go back to the implicit & explicit calculation option. Is that right?

 

Jun

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Jun Yang

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Oct 23, 2021, 6:54:11 PM10/23/21
to NMR POKY/SPARKY USER GROUP
By "refining constraints" you do mean to relax NOE constrains, right?   Jun

Lee, Woonghee

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Oct 23, 2021, 6:55:03 PM10/23/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Dear Jun,

 

Yes, and disabling if that is totally wrong.

 

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: Saturday, October 23, 2021 at 4:54 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]By "refining constraints" you do mean to relax NOE constrains, right?   Jun

Jun Yang

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Oct 23, 2021, 7:03:04 PM10/23/21
to NMR POKY/SPARKY USER GROUP
I don't include pdb from any of the implicit or explicit results for constrains-only-x calculation, right? And what do you mean to "disabling"?   Jun

Lee, Woonghee

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Oct 23, 2021, 7:06:54 PM10/23/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun, do you use Poky Analyzer? Using the distance constraint validator of Poky Structure Analyzer, you can simultaneously view restraints on PyMOL and POKY spectral view and sort not so good constraints out. Then you click export button there to generate another set for the iteration. There’s the “Disable” button in the distance constraint validator. If you want to know more about it, find PONDEROSA-C/S videos from Youtube.

 

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: Saturday, October 23, 2021 at 5:03 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]I don't include pdb from any of the implicit or explicit results for constrains-only-x calculation, right? And what do you mean to "disabling"?   Jun

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Jun Yang

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Oct 23, 2021, 8:01:27 PM10/23/21
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That's exactly I'm being doing to relax the NOEs that having violation in majority of the structures. As I remember that you suggested not to include a pdb file in constrains-only-x calculation to prevent biased structure output. So I'll do it without any pdb from explicit or implicit results as I did earlier.

Thanks.

Jun

Jun Yang

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Oct 25, 2021, 1:15:37 PM10/25/21
to NMR POKY/SPARKY USER GROUP
Hi Woonghee,

While I'm getting close to zero distance violation by relaxing NOE distance constrains, there is little change to the other two terms, ie, repulsive and angle violations. How should I relax these two terms? Do they correspond to the VDW & CDIH terms in the "final_xplor_each_##.pdb.stats" file? Also which term in that statistics file does "angle constrains validator" adjust?

Also if I want to relax the other two constrains, should I relax one term at a time or I can relax multiples terms at the same time?

Thanks.

Jun

Lee, Woonghee

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Oct 25, 2021, 1:19:57 PM10/25/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

 

Congrats on getting closer. Yes, repulsive and angle violations correspond to VDW & CDIH violations. Often, VDW & CDIH are still related to surrounding distance constraints. You should see structures and distance constraints in PyMOL and see what causes unnatural squeezes. You work on distances first and when you cannot improve, work on angles.

 

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: Monday, October 25, 2021 at 11:15 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]

Hi Woonghee,

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Jun Yang

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Oct 25, 2021, 2:31:50 PM10/25/21
to NMR POKY/SPARKY USER GROUP
 I guess my question is how to "work on angles", by adjusting in the "angle constrains validator"  window? If so, which energy term that is associated in the final statistics file?    Jun

Jun Yang

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Oct 25, 2021, 2:35:26 PM10/25/21
to NMR POKY/SPARKY USER GROUP
Also I just found out that somehow all my spectra failed to display the peak ornaments. Can you check on that?    Jun

Lee, Woonghee

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Oct 25, 2021, 4:03:39 PM10/25/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

I am sorry to tell you but your questions are way too many for the general user support. Please keep in mind I am responsible for my research projects, mentoring group members and teaching duties as well. I am spending significant time answering your questions even in the weekend. To make your questions worthy to answer for me, please write a separate post for different matters with proper titles. That will help other users when searching something later and that will reduce the number of questions in the future.

 

I guess my question is how to "work on angles", by adjusting in the "angle constrains validator"  window? If so, which energy term that is associated in the final statistics file?

 

That is CDIH. You can expand and shrink and set min and max values.

 

Also I just found out that somehow all my spectra failed to display the peak ornaments. Can you check on that?

 

Check if you set your spectrum correctly in “up” window. Also, check “j-I”, too.

 

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: Monday, October 25, 2021 at 12:35 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] Re: Noe assignment with AUDANA/AUDASA automation

 

[External Email - Use Caution]Also I just found out that somehow all my spectra failed to display the peak ornaments. Can you check on that?    Jun

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