Dear Sylvain,
Wim Vranken will have to give the final answer, but meanwhile I can maybe
help a bit:
For the ambiguous case (HB2 and HB3 have the same shift) I think the
treatment is correct. If you see a peak, that generally means that your HN
is close to *one* of the HB, but you do not know which (how could you -
they have the same shift). Converting to HB* would seem to be OK. What do
you think the program should do here?
For the stereospecific and non-stereospecific case there is the problem
that XPLOR does not have different atom names for two cases, as far as I
know. Some programs use stereospecific atom names and then swops the
chirality around during structure determination. I admit that I do not
know how XPLOR distinguishes between stereospecific and
non-stereospecific, but for what it is worth I suspect that you would have
atom names HB2 and HB3 in eitehr case.
That is all from me. Over to Wim,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Mon, 15 Jul 2013, Sylvain wrote:
> Hi,
>
> I am trying to use the Format Converter (CNS) to produce a list of NOE restraints as a .tbl file, for XPLOR-NIH.
>
> Almost everything seems fine, excepted some non-stereospecific and ambiguous restraints, in particular the Hba/Hbb and Hb2/Hb3 atoms.
> In order to understand how the conversion works, I made a short list of restraints covering the 3 possible cases (as far as I understand):
>
> -20SerH-20SerHb2 and Hb3 when the two H have the same chemical shifts (ambiguous)
> -13AspH-13AspHba and Hbb when the two H have different chemical shifts and the stereospecific attribution is unknown (non-stereospecific)
> -12SerH-12SerHb2 and Hb3 when the two H have different chemical shifts and the stereospecific attribution is known (stereospecific).
>
> The restraints table from CCPNMR below seems OK:
>
> # Resonances Value Upper Limit Lower Limit Error Peaks Orig. Data Weight Items
> 4:0 20SerHa-20SerH 2.92816 3.51379 2.34253 1.17126 1 1.70346 1.00000 1
> 1:01 20SerH-20SerHb3 3.07877 3.69452 2.46302 1.23151 1 1.26077 1.00000 2
> 1:0 20SerH-20SerHb2 3.07877 3.69452 2.46302 1.23151 1 1.26077 1.00000 2
> 2:0 13AspHbb-13AspH 3.25661 3.90793 2.60529 1.30264 1 0.90013 1.00000 1
> 5:0 13AspHba-13AspH 3.43588 4.12306 2.74871 1.37435 1 0.65264 1.00000 1
> 3:0 13AspHa-13AspH 3.26322 3.91587 2.61058 1.30529 1 0.88924 1.00000 1
> 6:0 12SerHb3-12SerH 3.28157 3.93788 2.62526 1.31263 1 0.85982 1.00000 1
> 8:0 12SerHb2-12SerH 3.52050 4.22460 2.81640 1.40820 1 0.56399 1.00000 1
> 7:0 12SerHa-12SerH 3.11738 3.74085 2.49390 1.24695 1 1.16994 1.00000 1
>
> After conversion using the format converter, even using several combinations of options, I get always the following .tbl file:
>
> ASSI { 5} (( segid " A" and resid 20 and name HN )) ( segid " A" and resid 20 and name HB# ) 3.079 0.616 0.616 peak 5 weight 1.00000E+00 volume 1.60851E+07 ppm1 7.888 ppm2 3.927
>
> ASSI { 2} (( segid " A" and resid 13 and name HN )) (( segid " A" and resid 13 and name HB1 )) 3.257 0.651 0.651 peak 2 weight 1.00000E+00 volume 1.13177E+07 ppm1 8.322 ppm2 2.954
>
> ASSI { 1} (( segid " A" and resid 13 and name HN )) (( segid " A" and resid 13 and name HA )) 3.263 0.653 0.653 peak 1 weight 1.00000E+00 volume 1.12299E+07 ppm1 8.322 ppm2 4.599
>
> ASSI { 4} (( segid " A" and resid 20 and name HN )) (( segid " A" and resid 20 and name HA )) 2.928 0.586 0.586 peak 4 weight 1.00000E+00 volume 2.16814E+07 ppm1 7.888 ppm2 4.218
>
> ASSI { 3} (( segid " A" and resid 13 and name HN )) (( segid " A" and resid 13 and name HB2 )) 3.436 0.687 0.687 peak 3 weight 1.00000E+00 volume 8.22974E+06 ppm1 8.322 ppm2 2.793
>
> ASSI { 8} (( segid " A" and resid 12 and name HN )) (( segid " A" and resid 12 and name HB1 )) 3.282 0.656 0.656 peak 8 weight 1.00000E+00 volume 8.75041E+07 ppm1 8.015 ppm2 3.873
>
> ASSI { 6} (( segid " A" and resid 12 and name HN )) (( segid " A" and resid 12 and name HA )) 3.117 0.623 0.623 peak 6 weight 1.00000E+00 volume 1.46713E+07 ppm1 8.015 ppm2 4.219
>
> ASSI { 7} (( segid " A" and resid 12 and name HN )) (( segid " A" and resid 12 and name HB2 )) 3.520 0.704 0.704 peak 7 weight 1.00000E+00 volume 5.73975E+07 ppm1 8.015 ppm2 3.992
>
> It seems to me that there are two problems with the Hb protons:
> -the stereospecific / non-stereospecific information appears to be lost, since all Hb are named HB1 and HB2?
> -for the ambiguous assignment, it seems that it is converted into the "OR" function of XPLOR-NIH (also written HB#). However, it should be a stereospecific assignment of both protons instead?
>
> Could you please tell me if I misunderstood the Hb attribution principles or if I missed some options of the format converter to generate a .tbl file?
> Thank you for your help,
> Sylvain
>
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