Re: Representing the Brownian rotational diffusion tensor in Molmol, etc.

[Sebastien Morin]

Hi all ! I also like the Tensor representation of the diffusion tensor. If Molmol is a problem for connectivities and heteroatoms, why not change relax to output script for Pymol instead of Molmol ? This is just a proposition since I'm a Pymol user...  ;) http://pymol.sourceforge.net/ Pymol is open source, fully scriptable, written in Python and can run on either Linux, Windows or Mac... Cheers Sebastien Chris MacRaild wrote: On Thu, 2006-10-26 at 13:45 +1000, Edward d'Auvergne wrote: During discussions with James Horne, James helped with a lot of debugging of relax back in 2004 prior to relax being publicly released, a few ideas were raised about how to represent the diffusion tensor superimposed onto the 3D molecular structure. This representation would significantly help in the comparison of different diffusion tensors. To compare diffusion tensors, you really need to compare the eigenvalues (Dx, Dy, and Dz, or Dpar and Dper). However because the corresponding eigenvectors, the axes of the tensor, may not be the same between two tensors (they could be 90 degrees out), you really need to orient the diffusion tensor with respect to the molecule so that you can compare the correct eigenvalues. I'll send another post with a quick tutorial on diffusion tensors which may help if there were parts of this paragraph which didn't make sense. At minimum you need to have the eigenvector representing the unique axis of the spheroid tensors superimposed onto the structure in 3D, or the three eigenvectors (axes) of the ellipsoid. For the spheroids this could possibly be done by adding two bonded atoms into a PDB file, one at the center of mass, the other placed in the correct orientation at a scaled distance away from the center atom. Then you could use the 'neon' representation for them in Molmol. Extending on the idea, it could be possible to create a picture of the diffusion tensors in Molmol. This would look similar to the contours presented in Tensor. By calculating the center of mass, adding atoms to a PDB file, connecting them, and then using 'neon' or 'line' in Molmol, a polygon representation of the tensor could be created. This, combined with the new model-free analysis protocol encoded in the 'full_analysis.py' sample script, could be the final nail in Tensor's coffin ;) This is a nice idea - I like this feature of Tensor. 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 might try to implement these ideas into the 1.3 development line. Edward _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel -- ______________________________________ _______________________________________________ | | || Sebastien Morin || ||| Etudiant au PhD en biochimie ||| |||| Laboratoire de resonance magnetique nucleaire |||| ||||| Dr Stephane Gagne ||||| |||| CREFSIP (Universite Laval, Quebec, CANADA) |||| ||| 1-418-656-2131 #4530 ||| || || |_______________________________________________| ______________________________________

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