Angel Herraez wrote:
>Hi to all
>While playing with the PDB files for ribosome (1GIX, 1GIY), I have
>found that some RNAs get an interrupted line for backbone, trace and
>cartoon.
>
>First, the facts (files attached):
>
>1) tRNA, all atoms. 5 break points (residues 7-8, 15-16, 33-34, 37-
>38, 48-49). It seems that the cause is that the 3'O--P bond is not
>set between those due to too long a distance. I thought that could be
>the cause for the broken trace.
>I tried to use Jmol "connect" command, the bonds are created but the
>backbone is still broken.
>
>
right -- those biopolymers are created once per model. The P-O bonds are
indeed too long. So that's not great data.
Still, I consider this a bug in Jmol and have added a backup test to see
if the P-P distance is within range, even if the P-O bond is not connected.
$ measure 0.0 3.0 (_P) {_O and not connected(_P)} # O near P but not
connected to it
$ show measures
Measurement Information
distance 1.9208533 0.192 nm [4SU]8:D.P #4993 [A]7:D.O3*
#4960
distance 1.8961179 0.19 nm [C]16:D.P #5149 [G]15:D.O3* #5132
distance 1.9813652 0.198 nm [U]34:D.P #5510 [U]33:D.O3*
#5496
distance 2.2756577 0.228 nm [U]38:D.P #5592 [A]37:D.O3*
#5576
distance 1.9941924 0.199 nm [5MC]49:D.P #5800
[U]48:D.O3* #5786
You can see how wild these are by checking the P-O and P=O bonds:
$ print {_O and connected(_P)}.bonds.length # average PO bond
1.5099798
$ print {_O and connected(_P) and connected(1)}.bonds.length # average
P=O bond
1.4892987
$ print {_O and connected(_P) and connected(2)}.bonds.length # average
P-O bond
1.520643
These are more like what one would expect for PO bonds.
>Then I added CONECT records in the PDB file, and the backbone is now
>OK.
>
>
won't be necessary
>
>2) rRNA, only P atoms. 2 break points (residued 1-2, 69-70).
>Similar situation, but given there are only P atoms, no bond can be
>created, so I don't find a way to fix the broken trace.
>
>
>
Just an abnormally long P-P distance. I've upped that maximum to 8.0
Angstroms. I can't see why not to. It was 7.5. This was arbitrary, based
on known structrures.
>My thoughts:
>I think that irrespective of bonds, if residue numbers are
>correlative, the backbone should be established. And particularly so
>in P-only models, where there are no bonds anyway.
>
>I will welcome opinions and suggestions to fix this and have a proper
>continuous trace.
>
>
Or, is it the opinion that this is NOT a bug and the trace should NOT
complete when the P-P distance is so long?
>
>
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> Date: 19 Nov 2007, 13:01
> Size: 2404 bytes.
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Northfield, MN
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