Hello! I would like to ask for advice and starting directions to be able to parse a new file format in Chimera so I can use Chimera's tools and generate images. The file format that I want to be able to open is generated from the Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ ) The AIMAll program of course can also do visualization and is very good at it. I am attaching an example of how a molecule looks. The problem is that if you want to work with big biomolecules (like DNA), the program is not very good to cloak/hide/select atoms so you have to click atom by atom to hide it and make some sense of the visualization. So, I will try to make a parser (or something that you would recommend) to open the file in Chimera and use Chimera's masking rules to select/deselect, hide/show atoms, which is very powerful. The text output generated by AIMAll has an XYZ list for each atom like this: Nuclear Charges and Cartesian Coordinates: ------------------------------------------------------------------------------- Atom Charge X Y Z ------------------------------------------------------------------------------- C1 6.0 0.0000000000E+00 2.3265459100E+00 0.0000000000E+00 C2 6.0 0.0000000000E+00 0.0000000000E+00 1.7647056500E+00 C3 6.0 0.0000000000E+00 0.0000000000E+00 -1.7647056500E+00 H4 1.0 1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 H5 1.0 -1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 C6 6.0 -2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H7 1.0 -2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H8 1.0 -3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 C9 6.0 2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H10 1.0 2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H11 1.0 3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 H12 1.0 0.0000000000E+00 0.0000000000E+00 3.8040484300E+00 H13 1.0 0.0000000000E+00 0.0000000000E+00 -3.8040484300E+00 That is easy, I think. But as you can see from the attached image, I want to be able to visualize the green spheres (which are called critical points and represents special properties of the electron density, extracted from quantum mechanical calculations). Those points are represented in the output file as: CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00 -9.60854463947958E-01 Type = (3,-1) BCP C1 C3 Rho = 2.4067790431E-01 GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14 HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01 3.5682199801E-01 HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01 7.8991714842E-01 HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01 6.1321358320E-01 DelSqRho = -5.2432458207E-01 Bond Ellipticity = 1.0071370222E-02 V = -2.5219393995E-01 G = 6.0556397216E-02 CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00 1.96757752864282E-18 Type = (3,-1) BCP H4 C1 Rho = 2.9524693796E-01 GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18 HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01 4.1039750300E-01 HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01 0.0000000000E+00 DelSqRho = -1.1711322730E+00 Bond Ellipticity = 9.3591342377E-03 V = -3.7782718105E-01 G = 4.2522056404E-02 etc etc etc First line indicates the critical point number followed by the XYZ coordinate of the point, and the second line shows which atoms are involved between that critical point. The rest is the electronic properties of the critical point (nothing to visualize there) So, I am guessing that the critical points can be represented as dummy atoms in Chimera following the XYZ coordinates? The idea is that first the molecule coordinates are parsed and the molecule is displayed and then display the critical points of each atom. If possible, show lines joining atoms that have a critical point between them... I know it is a difficult task, but maybe you can provide some starting directions? Anything will help because right now is double clicking 1000+ atoms! Thank you so much and have a good day, Rodrigo. ------------------------- Rodrigo Galindo-Murillo, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax)
