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. Then I added CONECT records in the PDB file, and the backbone is now OK. 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. 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.
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Date: 19 Nov 2007, 13:01
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