Messages

1

General discussions (Q&As) / idealizing DNA geometry of existing model

« on: June 30, 2015, 10:52:20 am »

Hi - I was wondering if there is a way to 'idealize' the geometry of a DNA model - in terms of pushing it towards B-form and C2'-endo sugar puckering? I have tried using 'find_pair *.pdb stdout | analyze stdin; x3dna_utils cp_std BDNA; rebuild -atomic bp_step.par *.pdb' and this provides a pdb file where the sugar pucker is corrected, and there are more sections which are B-form - however, the co-ordinates are shifted away from their current positions (and not all DNA sections are shifted in the same manner) and the chains are also renamed. I'm working on quite a large protein:DNA complex model to fit into an EM map and so would like to maintain the location and chain ID of the DNA co-ordinates and improve the geometry (to aid 'refinement' of this model against the EM map). What would be the best way to do this? Many thanks in advance!!