[Chimera-users] Parsing a new 3D file format

ros rodrigogalindo at gmail.com
Mon Jan 5 13:33:01 PST 2015


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)
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