correlation between entries in distance/angle constrain validator and final statistics

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Jun Yang

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Oct 26, 2021, 9:38:50 AM10/26/21
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Hi Colleagues,

I'm a little confused about the entries in these two constrain validator windows and corresponding sections in the final statistics file "final_xplor_each_##.pdb.stats". In my understanding, the tables of "violations in NOEPot term noe  ( 20 structures )" and "violations in XplorPot term CDIH  ( 20 structures )" should be the summary of the two validator windows, right? If so, my noe violation table has following:

viol%  amount  index    restraint name
---------------------------------------------------------------------------
  60.0   0.52  1891  (  resid  257 and name HD1*  ) (  resid  258 and name   HN  )
  25.0   0.50     9  (  resid  129 and name HG2*  ) (  resid  129 and name  HA*  )
  25.0   0.98  1739  (  resid  246 and name  HA*  ) (  resid  248 and name   HN  )
  25.0   0.57  2381  (  resid  294 and name  HA*  ) (  resid  294 and name  HG*  )
...

But in the "distance constraint validator", I have tons of noe entries that violate in more than 12 models. The same situation is also found in "angle constraint validator" where much more entries are violated than the summary in statistical file. Do I misunderstand something here?

Thanks for your help.

Jun
I

Lee, Woonghee

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Oct 26, 2021, 10:04:20 AM10/26/21
to Jun Yang, NMR POKY/SPARKY USER GROUP
Look on the violation amount. .stats is after applying the tolerance (0.5A and 5 degree). Also, the distance constraint validator evaluates on averaged coordinates for methyls. That is covered somewhere in NMRFAM workshop videos.

Woonghee


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From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
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Subject: [NMR POKY/SPARKY] correlation between entries in distance/angle constrain validator and final statistics
 
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Jun Yang

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Oct 26, 2021, 10:36:36 AM10/26/21
to NMR POKY/SPARKY USER GROUP
So I should use the final statistics as a base to relax the constrains, right?

By the way, is the nmrfam server up running? I submitted a job at 9:20am and still didn't receive a submission email after over an hour.

Thanks.

Jun

Lee, Woonghee

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Oct 26, 2021, 10:48:22 AM10/26/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

So I should use the final statistics as a base to relax the constrains, right? 

 

Because the current statistics is just a reference to the current structure which is intermediate, it gives you some level of idea what restraints disagree with the *intermediate* structures. That means still scientists’ insights should be put in and the file is only one of many clues. Same way, the information you get from validator windows, too. If you intend to fix some restraints to satisfy the structure you have right now, then yes.

 

Storage disks are full. Try a few hours later.

 

Woonghee

 

--

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

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

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Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

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Shipping/Mailing Address:

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From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Tuesday, October 26, 2021 at 8:36 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] correlation between entries in distance/angle constrain validator and final statistics

 

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So I should use the final statistics as a base to relax the constrains, right?

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Jun Yang

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Oct 26, 2021, 11:00:00 AM10/26/21
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Hi Woonghee,

Thanks for the information. That's very helpful. Can you send me a notice when the server is ready so that I can submit the job again?

Bests,

Jun

Lee, Woonghee

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Oct 26, 2021, 1:09:15 PM10/26/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

It is good to go. But it will be slower for a while.

 

--

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, October 26, 2021 at 9:00 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] correlation between entries in distance/angle constrain validator and final statistics

 

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Hi Woonghee,

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Jun Yang

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Oct 26, 2021, 1:31:29 PM10/26/21
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Thanks.    Jun

Jun Yang

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Oct 26, 2021, 8:21:39 PM10/26/21
to NMR POKY/SPARKY USER GROUP
I finally got a result of zero distance violation. Then I went ahead to look at the angle constrain validator.

In the final statistics I have these:
violations in XplorPot term CDIH  ( 20 structures )
viol%  amount  index    restraint name
---------------------------------------------------------------------------
 100.0  29.82   261        288  ALA  N         288  ALA  CA        288  ALA  C         289  SER  N   
 100.0  16.26   262        288  ALA  C         289  SER  N         289  SER  CA        289  SER  C   
  75.0   8.80   231        271  VAL  C         272  GLY  N         272  GLY  CA        272  GLY  C   
  75.0   5.98   314        317  PHE  N         317  PHE  CA        317  PHE  C         318  ALA  N   
  25.0   7.57   271        293  GLY  C         294  GLU  N         294  GLU  CA        294  GLU  C   
  20.0   7.28   123        207  GLY  N         207  GLY  CA        207  GLY  C         208  ARG  N   
...

But in the angle constrain validator I have no violations for all above phi/psi angles. Is there something wrong?

Anyway, I decide to add the range of the first two entry with 20 degrees for 1st and 10 degrees for 2nd. When I save the result, it generate a "postprocessed.aco" file under a new folder "PostVal", which is in quite a different format when compared "aco.tbl" or "aco.tbl.aco" in the original result folder. Is this the one I'll use together with the upl file for next run of "constrains-only x" calculation?

Thanks.

Jun

Lee, Woonghee

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Oct 26, 2021, 11:22:30 PM10/26/21
to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

 

Two things.

 

  1. Your angle violation can still be caused by distance constraints.
  2. Your first sequence is not 1.

 

I will take a close look on it when I have the time, but you want to play with distance constraints first. Secondly, you can fix final.aco, rename to something else and use it. .aco file is the DIANA format and basically C(i-1) – N(i) – CA(i) – C(i) is PHI(i) and N(i) – CA(i) – C(i) - N(i+1) is PSI(i).

 

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, October 26, 2021 at 6:21 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] correlation between entries in distance/angle constrain validator and final statistics

 

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I finally got a result of zero distance violation. Then I went ahead to look at the angle constrain validator.

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Jun Yang

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Oct 27, 2021, 12:50:06 AM10/27/21
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Hi Woonghee,

Thanks for the information. When calculating with new range, do I need to convert the angle if it is beyond the [-180,180] range, eg, convert 220 to -140?

Best,
Jun

Lee, Woonghee

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Oct 27, 2021, 11:57:03 AM10/27/21
to Jun Yang, nmr-s...@googlegroups.com

You can still stick with 220.

 

Personally, I wouldn’t change that way.

 

Let say if you change to

170 – 220

 

to

 

170 – -140

 

that can confuse me later to

 

-140 – 170

 

So, I would stick with 220. But it is up to you.

 

 

--

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, October 26, 2021 at 10:50 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] correlation between entries in distance/angle constrain validator and final statistics

 

[External Email - Use Caution]

Hi Woonghee,

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Lee, Woonghee

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Oct 27, 2021, 12:42:37 PM10/27/21
to Jun Yang, nmr-s...@googlegroups.com

Jun,

 

I have updated Poky Analyzer in the latest update (BUILD 08/17/21d). You will be able to use non-1 starting sequence for the angle constraint validator window.

 

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

 

Jun Yang

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Oct 27, 2021, 2:41:54 PM10/27/21
to NMR POKY/SPARKY USER GROUP
Thanks for the update.   Jun
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