> In the new PDB file, which by default could be called 'tensor.pdb',
> the atoms could all be set to a new residue called 'TNS' (an abbrev.
> of tensor). The residue could be setup using the HET, HETNAM, and
> FORMUL records, each atom could be represented by a HETATM record,
> followed by the TER record, and then all the atoms joined up by CONECT
> records. The file could be terminated with the MASTER and END
> records. Would anyone know how to get Molmol 2K to recognise the
> CONECT records as being bonds???
I've never tried too hard, but generaly found Molmol to be pretty
terrible at dealing with HETATMs and CONECT records. An alternative in
molmol would be to use the addDrawobj and moveDrawobj commands in a
macro to add and position the required lines. This would avoid having to
hack pdb files. I guess a third option would be the addTrajec command.
This adds a polyline connecting corresponding atoms in a series of
molecules (intended for illustrating MD trjectories).
I've just found out that 'CalcBond' will make Molmol accept the CONECT
records and generate the bonds. I wonder why don't they execute this
code when reading in the PDB file? The user shouldn't need to do
this. In Molmol using the bonds would be more useful than Drawobj
primitives. You can use multiple styles, colours, thicknesses, etc.
These abilities will be useful for creating a complex picture of the
tensor, possibly including Monte Carlo simulation results a la Tensor.
I already have the infrastructure in place in the
'branches/tensor_pdb' branch for creating these pseudo residues to
represent the diffusion tensor. In addition, this PDB file should be
useful for pymol, VMD, etc.
Edward
Re: Representing the Brownian rotational diffusion tensor in Molmol, etc.