Dear All, I have a pdb structure of a triple helix having a non-nucleotide residue conjugated between two residues of one of the strands. I would like to represent the backbone of all the three strands as a continuous tube. However, the tube of the modified strand gets interrupted right before and after the conjugate. I assume that pymol is not recognizing the atoms linking the non-nucleotidic modification to both ends of the strands as backbone atoms. The backbone in nucleic acids is P(i)-O5’(i)-C5’(i)-C4’(i)-C3’(i+1)-O3’(i+1)-P(i+1), in the case of my molecule the linkage is P(i)-O5’(i)-C5’(i)-C3’(i+1)-O3’(i+1). So the C4’ (and no other sugar atoms are present in the “modified” residue that is conjugate between the flanking nucleotides.
Is there any way to make Pymol consider some atoms as atoms of the backbone or to represent certain atoms like a “tube” or cartoon-like backbone? Thank you very much for you help. All the best, Miguel
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