On Dec 21, 2010, at 6:42 AM, Richard LAVERY wrote:
I am trying to visualize the graphic output from the Curves+ of a DNA duplex, which consists of two smooth backbone traces linked by vectors indicating the measured widths of the minor and major grooves. In the test case shown, adding two atoms defining one such vector and a single CONECT line linking them together (see attached PDB file) leads to three new bond vectors in the representation shown below. Am I making a mistake, or is this a problem with Chimera?
Hi Richard, The trick here is that Chimera will always connect consecutive residues contained in ATOM records unless there is an intervening TER record. That's where the two extra bonds are coming from: one between BACAD 1 and BACBD 2 and one between BACBD 2 and GRVAD 1. Ironically, the CONECT record you added was superfluous since Chimera would have automatically added a bond between GRVAD 1 and GRVAD 2! Your options to correct this are: 1) Add TER records between the residues 2) Use HETATM records instead of ATOM records. Chimera won't automatically join consecutive HETATM residues. --Eric Eric Pettersen UCSF Computer Graphics Lab