Author: bugman
Date: Tue Feb 19 17:10:22 2008
New Revision: 5026
URL: http://svn.gna.org/viewcvs/relax?rev=5026&view=rev
Log:
Copied the structure.create_diff_tensor_pdb() user function to
n_state_model.cone_pdb().
The function has been partly modified. The docstring needs to be rewritten
and the cone_type arg
supported.
Modified:
branches/N_state_model/prompt/n_state_model.py
Modified: branches/N_state_model/prompt/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/n_state_model.py?rev=5026&r1=5025&r2=5026&view=diff
==============================================================================
--- branches/N_state_model/prompt/n_state_model.py (original)
+++ branches/N_state_model/prompt/n_state_model.py Tue Feb 19 17:10:22 2008
@@ -26,7 +26,7 @@
# relax module imports.
import help
from specific_fns.setup import n_state_model_obj
-from relax_errors import RelaxBoolError, RelaxIntError, RelaxLenError,
RelaxListError, RelaxListNumError, RelaxStrError
+from relax_errors import RelaxBoolError, RelaxIntError, RelaxLenError,
RelaxListError, RelaxListNumError, RelaxNoneStrError, RelaxNumError,
RelaxStrError
class N_state_model:
@@ -116,6 +116,130 @@
n_state_model_obj.CoM(pivot_point=pivot_point, centre=centre)
+ def cone_pdb(self, scale=1.8e-6, cone_type=None, file='cone.pdb',
dir=None, force=False):
+ """Create a PDB file to represent the diffusion tensor.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ scale: Value for scaling the diffusion rates.
+
+ file: The name of the PDB file.
+
+ dir: The directory where the file is located.
+
+ force: A flag which, if set to 1, will overwrite the any
pre-existing file.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This function creates a PDB file containing an artificial geometric
structure to represent
+ the diffusion tensor. A structure must have previously been read
into relax. The diffusion
+ tensor is represented by an ellipsoidal, spheroidal, or spherical
geometric object with its
+ origin located at the centre of mass (of the selected residues).
This diffusion tensor PDB
+ file can subsequently read into any molecular viewer.
+
+ There are four different types of residue within the PDB. The
centre of mass of the
+ selected residues is represented as a single carbon atom of the
residue 'COM'. The
+ ellipsoidal geometric shape consists of numerous H atoms of the
residue 'TNS'. The axes
+ of the tensor, when defined, are presented as the residue 'AXS' and
consist of carbon atoms:
+ one at the centre of mass and one at the end of each eigenvector.
Finally, if Monte Carlo
+ simulations were run and the diffusion tensor parameters were
allowed to vary then there
+ will be multiple 'SIM' residues, one for each simulation. These are
essentially the same as
+ the 'AXS' residue, representing the axes of the simulated tensors,
and they will appear as a
+ distribution.
+
+ As the Brownian rotational diffusion tensor is a measure of the rate
of rotation about
+ different axes - the larger the geometric object, the faster the
diffusion of a molecule.
+ For example the diffusion tensor of a water molecule is much larger
than that of a
+ macromolecule.
+
+ The effective global correlation time experienced by an XH bond
vector, not to be confused
+ with the Lipari and Szabo parameter tau_e, will be approximately
proportional to the
+ component of the diffusion tensor parallel to it. The approximation
is not exact due to the
+ multiexponential form of the correlation function of Brownian
rotational diffusion. If an
+ XH bond vector is parallel to the longest axis of the tensor, it
will be unaffected by
+ rotations about that axis, which are the fastest rotations of the
molecule, and therefore
+ its effective global correlation time will be maximal.
+
+ To set the size of the diffusion tensor within the PDB frame the
unit vectors used to
+ generate the geometric object are first multiplied by the diffusion
tensor (which has the
+ units of inverse seconds) then by the scaling factor (which has the
units of second
+ Angstroms and has the default value of 1.8e-6 s.Angstrom).
Therefore the rotational
+ diffusion rate per Angstrom is equal the inverse of the scale value
(which defaults to
+ 5.56e5 s^-1.Angstrom^-1). Using the default scaling value for
spherical diffusion, the
+ correspondence between global correlation time, Diso diffusion rate,
and the radius of the
+ sphere for a number of discrete cases will be:
+
+ _________________________________________________
+ | | | |
+ | tm (ns) | Diso (s^-1) | Radius (Angstrom) |
+ |___________|_______________|___________________|
+ | | | |
+ | 1 | 1.67e8 | 300 |
+ | | | |
+ | 3 | 5.56e7 | 100 |
+ | | | |
+ | 10 | 1.67e7 | 30 |
+ | | | |
+ | 30 | 5.56e6 | 10 |
+ |___________|_______________|___________________|
+
+
+ The scaling value has been fixed to facilitate comparisons within or
between publications,
+ but can be changed to vary the size of the tensor geometric object
if necessary. Reporting
+ the rotational diffusion rate per Angstrom within figure legends
would be useful.
+
+ To create the tensor PDB representation, a number of algorithms are
utilised. Firstly the
+ centre of mass is calculated for the selected residues and is
represented in the PDB by a C
+ atom. Then the axes of the diffusion are calculated, as unit
vectors scaled to the
+ appropriate length (multiplied by the eigenvalue Dx, Dy, Dz, Dpar,
Dper, or Diso as well as
+ the scale value), and a C atom placed at the position of this vector
plus the centre of
+ mass. Finally a uniform distribution of vectors on a sphere is
generated using spherical
+ coordinates. By incrementing the polar angle using an arccos
distribution, a radial array
+ of vectors representing latitude are created while incrementing the
azimuthal angle evenly
+ creates the longitudinal vectors. These unit vectors, which are
distributed within the PDB
+ frame and are of 1 Angstrom in length, are first rotated into the
diffusion frame using a
+ rotation matrix (the spherical diffusion tensor is not rotated).
Then they are multiplied
+ by the diffusion tensor matrix to extend the vector out to the
correct length, and finally
+ multiplied by the scale value so that the vectors reasonably
superimpose onto the
+ macromolecular structure. The last set of algorithms place all this
information into a PDB
+ file. The distribution of vectors are represented by H atoms and
are all connected using
+ PDB CONECT records. Each H atom is connected to its two neighbours
on the both the
+ longitude and latitude. This creates a geometric PDB object with
longitudinal and
+ latitudinal lines.
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "n_state_model.cone_pdb("
+ text = text + "scale=" + `scale`
+ text = text + ", file=" + `file`
+ text = text + ", dir=" + `dir`
+ text = text + ", force=" + `force` + ")"
+ print text
+
+ # Scaling.
+ if type(scale) != float and type(scale) != int:
+ raise RelaxNumError, ('scaling factor', scale)
+
+ # File name.
+ if type(file) != str:
+ raise RelaxStrError, ('file name', file)
+
+ # Directory.
+ if dir != None and type(dir) != str:
+ raise RelaxNoneStrError, ('directory name', dir)
+
+ # The force flag.
+ if type(force) != int or (force != 0 and force != 1):
+ raise RelaxBinError, ('force flag', force)
+
+ # Execute the functional code.
+ n_state_model.cone_pdb(scale=scale, file=file, dir=dir, force=force)
+
+
def model(self, N=None, ref=None):
"""Set up the N-state model by specifying the number of states N and
the reference domain.
r5026 - /branches/N_state_model/prompt/n_state_model.py