The Display module

CamCASP cannot display graphics as Orient can, but it has a DISPLAY module that allows isosurfaces for molecules and atoms-in-molecules to be calculated. This data can be used to generate graphical views in Orient. Here we will see how to generate isosurfaces using CamCASP.

Syntax

For a molecular surface, the syntax is:

  BEGIN DISPLAY
    [MOLECULE {name}]
    [MAXPOINTS $N_{pts}$ | MAXTRIANGLES $N_{tri}$]
    MOLECULAR-DENSITY
     SLATER-MULTIPLIER [=] $M_{slater}$ (default 10.0)
     ISODENSITY $\rho$
     STEP [=] {step} [BOHR | ANGSTROM]
    END
  END

And for atomic surfaces it is

BEGIN DISPLAY
    [MOLECULE {name}]
    [MAXPOINTS $N_{pts}$ | MAXTRIANGLES $N_{tri}$]
    AIM-ATOMS
       ATOMS [=] [ALL | {list of atom names}]
       W-MIN [=] $W_{min}$
       R-MAX [=] $R_{max}$
       SLATER-MULTIPLIER [=] $M_{slater}$ (default 10.0)
       STEP [=] {step} [BOHR | ANGSTROM]
       [ANISO-ONLY]
       AIM-METHOD [DF | ISA ] [FUNC-EXPANSION | GRID-BASED ] [with] [RHO | RHO-C]
       ISODENSITY [=] $\rho$ (default 0.001)
       [PREFIX {file prefix}]
    END
END

For a description of each option see the User's Guide.

Example: Formamide

Here's part of the CamCASP command file for a set of isodensity surface calculations for the formamide molecule:

...
BEGIN DF
  Molecule formamide
  Type RHO
  Eta = 0.0
  Lambda = 1000.0
  Print only normalization constraints
  Solver GELSS Condition = 1e-15
END

Begin Multipoles
  Molecule formamide
  DF Type RHO with constraints
  Rank 4
End

Begin Display
  MOL-DENSITY
    SLATER-MULTIPLIER = 10
    DR = 0.2 BOHR
    DENSITY-METHOD RHO-C
    ISODENSITY = 0.01
    PREFIX formamide_aQZ_iso0.01
  END
End
Begin Display
  MOL-DENSITY
    SLATER-MULTIPLIER = 10
    DR = 0.3 BOHR
    DENSITY-METHOD RHO-C
    ISODENSITY = 0.001
    PREFIX formamide_aQZ_iso0.001
  END
End
...

The full file can be found here.

The output includes the files:

$   ls
HCONH2_aQZ-data-summary.data HCONH2_aQZ_camcasp.out       formamide_1.00E-04_iso.grid
HCONH2_aQZ.bash              formamide_1.00E-02_iso.grid
HCONH2_aQZ.cks               formamide_1.00E-03_iso.grid

The surfaces are included in the *.grid files which are of the form:

MOL-NAME  formamide
DENSITY-TYPE   RHO-C
UNITS BOHR
BEGIN SITES
    1          C    6.00     0.7369    -0.2902     0.0000
    2          O    8.00    -0.4197    -2.2642     0.0000
    3          N    7.00    -0.3376     2.0382     0.0000
    4         H1    1.00     2.8209    -0.2060     0.0000
    5         H2    1.00    -2.2333     2.1962     0.0000
    6         H3    1.00     0.7228     3.6114     0.0000
END SITES
STEP    0.30000000E+00
POINTS     4696
TRIANGLES     9388
BEGIN DATA
    -4.2000000     1.2000000    -0.7174596
    -4.2358335     1.2000000    -0.6000000
    -4.2000000     1.1315009    -0.6000000
    -4.2912392     1.2000000    -0.3000000
    ...
    ...
     5.5275866     0.0000000    -0.3000000
     5.5978608     0.0000000     0.0000000
     5.5275828     0.0000000     0.3000000
     5.4549442     0.3000000     0.0000000
       1       2       3
       2       4       5
       3       2       5
       4       6       7
       5       4       7
      ...
      ...
    4695    4696    4694
    4680    4695    4674
    4684    4678    4696
    4684    4696    4679
END DATA

The file contains a short molecule description and then the grid data as a set of points and index triplets that define the triangulation.