TALOS and ambiguous protons in POKY vs XPLOR-NIH
Anamika Gaur
Hi Prof. Lee,
I have two questions
Question 1 - About TALOS's version used in the PONDEROSA C/S vs on the NIH website
The TALOS results given in the output after using the PONDEROSA tool is different from the TALOS that is on the NIH website. To get around this, I generate a .aco file from the TALOS results (in the JRAMA viewer) that I get from the NIH website and add it under "Restraints" while using the POKY builder, the results from the PONDEROSA C/S vs the POKY builder are slightly different.
I was wondering why the TALOS results are different and if there is a
particular version that the PONDEROSA client is using?
Question 2 - About how POKY and XPLOR-NIH treat ambiguous protons
When I submit a job for structure calculation on PONDEROSA/POKY builder, how should my ambiguous protons be stored in the peak lists in POKY?
For example, I have HB2 and HB3 in Lysine, I currently have HB* (I have also tried to use QB as per the CYANA format) in POKY, and POKY does not pick this up as a placeholder for HB2 or HB3. I know that XPLOR-NIH uses the "OR" syntax or the wildcard nomenclature (HB* , * for any string so here for 2 and 3).
So naturally when I submit the job, I get an alert about my hydrogen completeness being less than 60%.
I do get a structure out though, but is there a way for me to see in the results, like at what iteration does XPLOR decide that a certain proton will be fixed at HB2 instead of HB3?
Thank you in advance for your help!
Sincerely,
Anamika
Lee, Woonghee
Hi,
Q1. You can check the version in the header part of the result file. It will be talos_out.tls. You can check the input file as well- talos_in.tab
Q2. In POKY, it is more advised to use PDB/BMRB nomenclature (HX2/3). When it comes to the ambiguity, just removing the last digit will do like HX12/HX13 -> HX1. Using Q or M will work as well. I prefer to just remove the last digit because it can be simply translated into XPLOR-NIH compatible formats by adding an wildcard *. PONDEROSA Server automatically handles formats for XPLOR-NIH, so the user can just stick with HX2/3.
Best,
Woonghee Lee, I.E.I.P., M.S., Ph.D.
Assistant Professor & Data Science and Chemistry Certificate Program Director
Department of Chemistry
University of Colorado Denver
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From:
nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Anamika Gaur <anamik...@gmail.com>
Date: Friday, September 5, 2025 at 7:51 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] TALOS and ambiguous protons in POKY vs XPLOR-NIH
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Anamika Gaur
Lee, Woonghee
Yes, it uses the offset parameter in case people doesn’t do reference correction. If you don’t want to use it, you can add .aco file of your own as inputs.
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