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CCPNMR  July 2013

CCPNMR July 2013

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Subject:

Re: Format Converter to XPLOR-NIH

From:

Rasmus Fogh <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Tue, 16 Jul 2013 17:50:14 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (80 lines)

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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