Rasmus Fogh wrote:
> Dear Christoph,
>
> Does sound a bit strange. I could think of some reasonable explanations,
> but I'd need to know more about the details before I could comment. We
> cannot guarantee the same behaviour as any one dynamics program - they
> have different data and a different situation - but, depending on what is
> happening, we might improve the documentation (or maybe the program?).
>
> Could you send us:
>
> What are the actual constraints in the restraint list?
>
13 705:0 558GluHa - 554LysHea 6.00000 6.00000 0
6.00000 1 0.78557 4.89602 0.25422 1.00000 None
ASSI { 8585}
(( segid " A" and resid 558 and name HA ))
(( segid " A" and resid 554 and name HE2 ))
6.000 4.200 0.000 peak 8585 weight 1.00000E+00 volume
5.61484E+06 ppm1 4.082 ppm2 2.408
> What is the corresponding peak assignment?
>
558Glu Ha, 558Glu Ca, 554 LysHea
> What other restraints do you have involving HEa and Heb?
>
Number # Resonances Value Upper Limit Lower Limit
Error Peaks Viol Struc Value Orig. Data Weight Details
1 714:0 554LysHda - 554LysHea 6.00000 6.00000 0
6.00000 1 None 2.07890 0.17681 1.00000 None
2 715:0 554LysHdb - 554LysHea 6.00000 6.00000 0
6.00000 1 None 2.07890 0.14570 1.00000 None
3 858:0 554LysHea - 554LysHba 6.00000 6.00000 0
6.00000 1 None 3.66386 0.06055 1.00000 None
4 987:0 554LysHea - 554LysHda 5.00000 5.00000 0
5.00000 1 None 2.07890 0.49580 1.00000 None
5 1017:0 554LysHea - 554LysHdb 6.00000 6.00000 0
6.00000 1 None 2.07890 0.25348 1.00000 None
6 1017:01 554LysHea - 554LysHgb 6.00000 6.00000 0
6.00000 1 None 2.12544 0.25348 1.00000
7 399:0 554LysHea - 555LeuHa 6.00000 6.00000 0
6.00000 1 0.04240 4.68904 0.09327 1.00000 None
8 858:01 554LysHea - 555LeuHba 6.00000 6.00000 0
6.00000 1 None 5.57662 0.06055 1.00000
9 280:0 554LysHea - 577TyrHd* 6.00000 6.00000 0
6.00000 1 None 4.62054 0.04235 1.00000 None
10 307:0 554LysHea - 577TyrHe* 6.00000 6.00000 0
6.00000 1 None 3.21095 0.08587 1.00000 None
11 718:0 554LysHga - 554LysHea 6.00000 6.00000 0
6.00000 1 None 2.12544 0.11747 1.00000 None
12 719:0 554LysHgb - 554LysHea 6.00000 6.00000 0
6.00000 1 None 2.12544 0.16499 1.00000 None
14 710:0 558GluHbb - 554LysHea 5.00000 5.00000 0
5.00000 1 None 3.25922 0.40758 1.00000 None
15 711:01 581IleHd1* - 554LysHea 6.00000 6.00000 0
6.00000 1 None 5.36364 0.01824 1.00000
> What are the actual distances HE2-HA and HE3-HA?
>
6.79A and 5.02A (though MolMol might have corrected the HB2-HB3
chirality). From the .pdb file: HE1-HA: 6.78 HE2-HA:5.021
> How do the various averaged distances come out in XPLOR and Analysis?
>
I cant say about Xplor though it must be below 6.3A since it doesn't
appear in any violation report for this structure. Analysis distances
are 4.89A (NOE sum) and 5.022A (min Dist).
> Thanks,
>
> Rasmus
>
Might it be that the CNS export via the format converter and the
structure import via Edit structures handle the HB1/HB2 to HB2/HB3
mapping differently ?
thanks for looking into this,
Christoph
---------------------------------------------------------
Dr. Christoph Brockmann
Division of Structural Studies
MRC Laboratory of Molecular Biology
Hills Road
Cambridge, CB2 2QH
phone: +44-1223-40-2261 or +44-1223-40-2068
e-mail: [log in to unmask]
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