Subsections


molmol.tensor_pdb

Image molmol

Synopsis

Display the diffusion tensor PDB geometric object over the loaded PDB.

Defaults

molmol.tensor_pdb(file=None)

Keyword arguments

file: The name of the PDB file containing the tensor geometric object.

Description

In executing this user function, a PDB file must have previously been loaded , a geometric object or polygon representing the Brownian rotational diffusion tensor will be overlain with the loaded PDB file and displayed within Molmol. The PDB file containing the geometric object must be created using the complementary structure.create_diff_tensor_pdb user function.

To display the diffusion tensor, the multiple commands will be executed. To overlay the structure with the diffusion tensor, everything will be selected and reoriented and moved to their original PDB frame positions:

SelectAtom `'
SelectBond `'
SelectAngle `'
SelectDist `'
SelectPrim `'
RotateInit
MoveInit

Next the tensor PDB file is read in, selected, and the covalent bonds of the PDB CONECT records calculated:

ReadPdb file
SelectMol `@file'
CalcBond 1 1 1

Then only the atoms and bonds of the geometric object are selected and the `ball/stick' style applied:

SelectAtom `0'
SelectBond `0'
SelectAtom `:TNS'
SelectBond `:TNS'
XMacStand ball_stick.mac

The appearance is finally touched up:

RadiusAtom 1
SelectAtom `:TNS@C*'
RadiusAtom 1.5


The relax user manual (PDF), created 2016-10-28.