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General discussions (Q&As) / non planar base pairs
« on: April 17, 2010, 01:19:28 pm »
Dear Xiang-Jun,
Another interrogation related to 3DNA. We came accross a strange base pair selected by find_pair, the base looks almost othogonal and this, although not frequent, is not a unique case (this base pair involves symmetry related residues). We used find_pair -p on a modified PDB file of the 1DC0 structure with following parameters:
Base-pair criteria used: 3.35 0.00 15.00 1.50 65.00 4.50 7.50 [ O N].
In which way should we change these parameters in order to eliminate such base pairs (thought stagger=1.5 would do)?
see attached files,
Best regards,
Pascal
Another interrogation related to 3DNA. We came accross a strange base pair selected by find_pair, the base looks almost othogonal and this, although not frequent, is not a unique case (this base pair involves symmetry related residues). We used find_pair -p on a modified PDB file of the 1DC0 structure with following parameters:
Base-pair criteria used: 3.35 0.00 15.00 1.50 65.00 4.50 7.50 [ O N].
In which way should we change these parameters in order to eliminate such base pairs (thought stagger=1.5 would do)?
see attached files,
Best regards,
Pascal