calculate charges

Specifies whether Chime should calculate atom charges. Charges are used to calculate potentials when showing MEP or MLP colors on a surface ("color list {listname} mep|mlp").

Syntax

calculate charges {true|false|refresh}

or
calc charges {true|false|refresh}

true - (default) if charges are needed for potential calcs (MEP for example) then they WILL BE calculated if there is NO negative/positive temperature data in PDB file, or no charges in MOL, etc. file. (if there are negative values in PDB file charge data then Chime will not caclculate charges by default. See "refresh" below for FORCING recalculation of charges).

false - Prevents Chime from recalculating charge data (and overwriting PDB file temperature data). This option allows the user to use any PDB file temperature data for MEP calcs.

refresh - Forces the recalculation of charges for the current structure. This can be useful for forcing the overwriting of PDB temperature data, or after a "set charge function" command.

center xyz

Sets the zoom/translate center to a specific point, rather than a specific atom.

Syntax

center xyz #x# #y# #z#

#x# - the x coordinate.

#y# - the y coordinate.

#z# - the z coordinate.

color dots mep

Can be used to color dots based on MEP calculations.

Syntax

color dots mep

color list

Colors a surface using a specific type of mapping and specific colors.

Syntax

color list {listname} [save] {list color command}

or
color list {listname} [colors] {list of colors only}

or
list {listname} color {list of colors only}

listname - name of the surface, assigned in the "surface", "load pmesh" or "load surface gaussian" command that creates the surface.

save - optional keyword that tells Chime not to recalculate the specified property if it has already been calculated, but to update the color map used for texturing. This can be much faster for experimenting with alternate coloring schemes.

colors - optional keyword indicating that what follows is a list of colors, not a color command.

The list color commands are as follows:

Command	Qualifier	Description
mep or potential		Color surface using Molecular Electrostatic Potential calculations. Up to 9 colors can be specified. If multiple colors are specified, they are used to represent different MEP energies along a continuum from lowest to highest. The special color clear or transparent denotes parts of the texture map that will not be rendered.
	rasmol	(optional) Use rasmol potential coloring scheme instead of default red-white-blue schema.
	iso	(optional) Use isocontour coloring scheme. This qualifier requires addional arguments, syntax: iso #number# [contourcolor maincolor lowestband_color highestband_color] If the #number# is an integer, then it specifies the number of contour lines over the whole range. If #number# has a decimal point, it specifies the size of the divisions between contour lines. The maincolor defaults to white, the contourcolor to black. The high/low colors, because they also default to white, do not appear.
mlp		Color list using Molecular Lipophilicity Potential calculations.
	See mep	The same qualifiers are used as in mep.
center		Color list based on distance from origin (center). If multiple colors are specified, they are used to represent different distances from shortest to longest.
distance	#distance#	Color list based the distance to the nearest selected atom divided by the specified distance. Anything near or greater than specified distance gets mapped to the last texture map color specfied.
	see mep	The same optional qualifiers are used as in mep.
atom		Color list based on the closest atom's color. This can be used after the various atom/residue coloring commands to color the surface in interesting ways.
selected		Turn ON/OFF display of surface within/outside a specified distance from the nearest selected atom. Syntax: selected [distance] [within On|Show|Off|Clear] [outside On|Show|Off|Clear] For example, "color list test selected 6.0 On Off" would turn the parts of surface "test" ON that are within 6.0 angstroms of the nearest selected atom, and the parts of the surface OFF that are outside that range.

The default color scheme for a Gaillard MEP or MLP calculation is as follows:

Color	Actual Value	Normalized
Red	-infinity	-0.50 - -0.39
Purple		-0.39 - -0.28
Orange		-0.28 - -0.17
Yellow		-0.17 - -0.06
White	0	-0.06 - 0.06
Cyan		0.06 - 0.17
Green		0.17 - 0.28
GreenBlue		0.28 - 0.39
Blue	infinity	0.39 - 0.50

label residue

Specifies whether to label selected residues.

Syntax

label residue {true|false}

or

label residue (same as label residue true)

true - label the selected residues.

false - (default) do not label the selected residues.

list

Sets list visibility.

Syntax

list {listname} {true|false}

true - (default) make the list visible.

false - make the list invisible.

list color

Sets the list color. This is identical to the "color list {listname} colors" command; see color list for details.

Syntax

list {listname} color

list transparent

Sets the list transparency value.

Syntax

list {listname} transparent {true|false}

true - make the list transparent.

false - (default) make the list opaque.

list zap|delete

Deletes the specified list.

Syntax

list {listname} zap

or

list {listname} delete

The * character can be used as a simple wildcard. For example, "list * delete" deletes all lists; "list amino* delete" deletes all lists whose name starts with "amino".

load pmesh

Loads a pmesh file, creating a surface.

Syntax

load pmesh {filename} [listname]

The optional listname can be used in subsequent commands to refer to the surface created by this command. Right?

load surface gaussian

Loads a Gaussian file, creating a surface.

Syntax

load surface gaussian {filename} [listname]

The optional listname can be used in subsequent commands to refer to the surface created by this command. Right?

sculpt

Sends a command to Sculpt to be processed by that program.

Syntax

sculpt {command}

or

send sculpt {command}

Everything after sculpt is sent for Sculpt to interpret.

set charge

Sets the specified charge on all selected atoms. Use this to specify your own charge/other data, so that the MEP functions can map these values onto a texture mapped surface.

Syntax

set charge {charge value}

set charge function

Sets the specific charge calculation function to use for calculating charges for molecules which do not have charge information present.

Syntax

set charge function {none|Gasteiger|Kollman|Charmm}

none - (default) Chime will choose the charge function based on the number of heteroatoms in the structure:

If >=255 atoms and hydrogens present in a PDB, then Kollman partial charges are assigned for standard residues/atoms.

If >=255 atoms and Kollman partial charges are not used and aminoacids are present, then Charmm 1.9 charges are assigned.

If >=255 atoms and neither Kollman nor Charmm was used, then Gasteiger is used.

If <255 atoms, then Gasteiger is used.

Gasteiger - uses Gasteiger's method of assigning partial charges.

Kollman - assigns Kollman partial charges to standard aminoacid and nucleic residues. This requires hydrogens to be present in the PDB file.

Charmm - assigns Charmm 1.9 charges to aminoacids only.

set clear color

Sets the color to use when blending a "clear" section of texture map with another color. The default is white.

For example, the command "color list text center red clear blue" yields red->white for the first third, clear for the middle third, and white->blue for the last third. What does white->blue mean? What kind of gradation is used?

The command "color list test center clear red" yields clear for the bottom half, and white->red for the top half.

Syntax

set clear color {color}

or

set transparent color {color}

set gaussian contour

Sets the contour level used when reading gaussian data files. The default contour level is 0.2 A.

Syntax

set gaussian contour {value}

value - real value in Angstroms.

set load check

By default, Chime / Chime Pro 2.0 will not execute a load command if the same molecule is being re-loaded. By calling "set load check false", you can override this feature, allowing the molecule to be re-loaded.

This also has an effect on the list zap command. When load check is set to true (the default), list zap will be ignored because an implicit zap is done when loading a new molecule.

Syntax

set load check {true|false}

set mep|mlp function

Specifies the function used to determine MEP or MLP distance when rendering a surface.

This command is often used in conjunction with "set mep|mlp distance" to establish a distance "cutoff".

Syntax

set mep function {1 or Gaillard|2 or Audry|3 or Fauchere|4 or Hartshorn|5 or Coulomb}

or

set mlp function {1 or Gaillard|2 or Audry|3 or Fauchere|4 or Hartshorn}

Some of the calculations used:

Function	Description
Gaillard or 1	MLP = Sum(f * e^(-d/2))1-natoms f = Lipophilic value for atom i d = distance from point to atom (angstroms) Gaillard, P., Carrupt, P.A., Testa, B. and Boudon, A., J.Comput.Aided Mol.Des. 8, 83-96 (1994)
Audry or 2	MLP = Sum(f/(1 + d))1-natoms f = Lipophilic value for atom i d = distance from point to atom (angstroms) Audry, E.; Dubost, J. P.; Colleter, J. C.; Dallet, P. A new approach to structure-activity relations: the "molecular lipophilicity potential". Eur. J. Med. Chem. 1986, 21, 71-72.
Fauchere or 3	MLP = Sum(f * e^(-d))1-natoms f = Lipophilic value for atom i d = distance from point to atom (angstroms) Fauchere, J. L.; Quarendon, P.; Kaetterer, L. Estimating and representing hydrophobicity potential. J. Mol. Graphics 1988, 6, 203-206.
Hartshorn or 4	Mike Hartshorn's weighted distance algorithm
Coulomb or 5	Coulomb's law distance function (same as rasmol potential distance function)

set mep|mlp distance

Sets the maximum distance to be considered for MEP or MLP influence calculations. The default is 8.0 angstroms.

Syntax

set {mep|potential} [distance] [within] #angstroms#

or

set mlp [distance] [within] #angstroms#

Use the keywords mep and potential interchangably in this command.

Either distance or within is required, but not both.

set mep mode

Set the range for MEP texture mapping.

Syntax

set mep mode {1|2|3 or rasmol}

mode 1 - surface is colored relative to extremes of molecule.

mode 2 - (-0.10) to +0.10 range for charges

mode 3 - (-0.24) to +0.24 range for charges (what rasmol uses)

set mlp mode

Sets the mode for mlp texture map calculations to either "absolute" or "relative".

Syntax

set mlp mode {true|false}

true - absolute scale, for comparing different molecules.

false - (default) relative scale, highest/lowest is relevant to the current molecule only.

set picking select

Allows the user to select and deselect objects using the mouse. If objects are already selected beforehand, that selection can be added to or modified by the user.

Only one type of object can be selected at a time, depending on the qualifier used in the command.

Syntax

set picking select {atom|bond|chain|residue}

or

set picking select (same as set picking select atom)

set spin fps

Sets the spin frames per second. This is equivalent to the spinfps embed tag.

Syntax

set spin fps ###

set spin x|y|z

Sets the speed of spin along the x, y, or z axis, in degrees per second. This is equivalent to the spinX, spinY/ and spinZ embed tags.

Syntax

set spin {x|y|z} ###

show atom|residue|chain|model

Shows objects of the specified type.

Syntax

show {atom|residue|chain|model} [all] [identify]

If the all qualifier is present, all objects of the specified type are shown. Otherwise, only the selected objects of that type are shown.

If the identify qualifier is present, then each atom/chain name is shown as well.

show mlp

Shows MLP totals, and sum of +/- contributions, based on either SURFACE values, or VDW dots values, depending on what was used with the last MEP coloring command.

Syntax

show mlp

show list

Lists the names of all display lists. If used with the optional all qualifier, also gives complete information about the display lists, including types and numbers of objects in the lists.

Syntax

show list [all]

show selected

Turns on/off the "highlight selection" feature, in which all of the selected objects are colored gold.

Syntax

show selected {true|false}

or

show selected (same as show selected true

show spin

Reports "spin on" or "spin off" via the MessageCallBack EMBED tag option.

Syntax

show spin

spin save|restore

Used to save the current spin state, then restore it at a later time.

Syntax

spin {save|restore}

spin true|false

Turns spin on and off.

Syntax

spin {true|false}

or

spin (same as spin true)

surface

Creates a surface with specified properties.

Syntax

surface [name] [color] [spacing] [probe radius] [surface smoothing true|false]

name - name assigned to the surface for use in subsequent script commands.

color - initial color given to the surface.

spacing - ... The default spacing depends on the number of atoms in the file:

Atoms	Default Spacing
<=255	0.3 A
256-499	0.55 A
500-749	0.65 A
750-999	0.75 A
1000+	0.80 A

probe radius - The default is 1.4 A.

surface smoothing -

zap true

Allows deletion ("zap") of a list, even when in "set load check true" mode where list zap is normally ignored.

Syntax

zap true