RNA strucuture analysis error

[ouyangdf]

Dear all,

 Recent I analyze one RNA structure from Material Studio4.3 and find it doesnot work. I define the base in the baselist.dat, but it still doesnot
 work. I attach the file and could you give me some advices? Thanks very much for your help!

Regards,
Ouyang

[xiangjun]

Dear Ouyang,

I am not familiar with Material Studio4.3 you used to generate the RNA structures. However,  thanks to your attached PDB file, I could check why 3DNA did not work. As is clear from the RasMol rendered image (attached below),  your RNA structure is heavily distorted.  To make my point even clearer, I extracted base-pair A51 vs U33 (coordinates attached) and rendered it with RasMol (also attached below): note the extra-erroneous connections in A, and the non-planar geometry of U. Moreover, the distance of N6(A)...O4(U) is 4.9 A, and N1(A)...N3(U) is 5.6 A.

Based on my experience, I would hardly take this as a valid pair at all. Still, if you define A51 and U33 in 'baselist.dat' and set H-bond distance cut-off to 5.0 A instead of the default 4.0 A in 'misc_3dna.par'

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# Section 1: parameters defining H-bonding, in angstrom
#   primary H-bond
<hb_dist1>5.0</hb_dist1>A51 and U33 will still be identified as a pair:

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   1    2  1 #    1 + ....>-:...0_:[A51]a-**--u[U33]:...0_:-<....  3.47  1.12 43.35 10.92  7.88
##### Base-pair criteria used:   5.00   0.00  15.00   2.50  65.00   4.50   7.50 [ O N]HTH,

Xiang-Jun

[attachment=2:1psgyjp7]ARNA-ms.png[/attachment:1psgyjp7]
[attachment=1:1psgyjp7]ARNA-bp1.png[/attachment:1psgyjp7][attachment=0:1psgyjp7]ARNA-bp1.pdb[/attachment:1psgyjp7]

[ouyangdf]

Dear Xiang Jun,

Thanks very much for your kind help! I will try it as your advice.

Regards,
Ouyang