| Count ligand hits with FRONT/BACK side of surface region |
| Version 2.72 April 28 2004 |
|
{COUNT[ligand_name, existing_region, FOR_EACH_TIME_STEP, ALL_HITS_FRONT]}=>outfile.name
or
{COUNT[ligand_name, existing_region, FOR_EACH_TIME_STEP, ALL_HITS_BACK]}=>outfile.name
|
|
This COUNT statement let user count the collision of the ligand with either FRONT or BACK side of the surface region. The
FRONT/BACK side of the surface is defined by the right-handed rule of the Cartesian Coordinate System.
|
| Count hits of ligand with surface region |
| Version 2.71 November 26 2003 |
|
{COUNT[ligand_name, existing_region, FOR_EACH_TIME_STEP, ALL_HITS]}=>outfile.name
|
|
New reation output format available for user to count
ligand hits with the surface region. The COUNT syntax is as above.
|
| VOXEL_VOLUME_MODE |
| Version 2.70 November 26 2003 |
|
VIZ_DATA_OUTPUT {
MODE = VOXEL_VOLUME_MODE
iteration_specifiers
...
} |
|
This mode outputs counts of molecule states contained within a voxelized volume model space.
|
| Repartition space after checkpoint |
| Version 2.69 September 03 2003 |
|
| Start from MCell version 2.69, user can ajust the partitioning after checkpoint.
|
| Count reaction data on defined surface region |
| Version 2.69 September 03 2003 |
|
| Start from MCell version 2.69, you can count chemical
reactions as what you did in the previous MCell version to the
defined surface region. The syntax is the same as you count on
WORLD, just replace WORLD with name of the "existing_region".
For details please check MCell documentation.
|
| TIME_LIST function for the visualization output |
| Version 2.57 December 16 2002 |
|
REACTION_DATA_OUTPUT {
TIME_LIST=time_list_specifier
{COUNT [ count_what, count_where, count_how, ...]
...} => file_name
...
}
VIZ_DATA_OUTPUT {
MODE= ...
TIME_LIST=time_list_specifier
...
} |
The TIME_LIST can be applied to both the visualization output and the
reaction data output. This function use the real simulation
time (unit: seconds) to select the output time. You can not use
the TIME_LIST expression and the ITERATION_LIST or STEP in a same
function at the same time. The time_list_specifier has three formats:
- TIME_LIST=[t1, t2, t3,
... , tm]
- TIME_LIST=[[tstart TO tstop STEP tstep]]
- TIME_LIST=[[tstart TO tstop STEP
tstep],tm, ... , tn]
Where t1, t2,t3, tm are real numbers that represent the time (seconds) in the simulation. |
| ITERATION_LIST expression avaliable for the chemical reaction output |
| Version 2.56 September 16 2002 |
|
REACTION_DATA_OUTPUT {
ITERATION_LIST=iteration_list_specifier
{COUNT [ count_what, count_where, count_how, ...]
...} => file_name
...
} |
The iteration_list_specifier has the following three formats, they all use simulation
iteration number to choose the time to output data:
- ITERATION_LIST=[n1, n2,
n3, ... , nm]
- ITERATION_LIST=[[iterationstart TO
iterationstop STEP iterationstep]]
- ITERATION_LIST=[[iterationstart TO
iterationstop STEP iterationstep],
nk, nl, ... , nm]
Where n1, n2,n3,
nm are integer numbers that represent the iteration
number in the simulation.
|
| New function of the MCell Visualization mode: VOXEL_IMAGE_MODE |
| Version 2.55 August 30 2002 |
|
VIZ_DATA_OUTPUT {
MODE = VOXEL_IMAGE_MODE
iteration_specifiers
...
} |
| This function let user to output pgm(portable graymap format) images
right-side-up and teach it to voxelize effector states as well as
ligand states.
|
| New mathematical functions in MDL |
| Version 2.54 August 14 2002 |
|
x = MIN(y,z)
x = MAX(y,z)
x = CEIL(y)
x = FLOOR(y)
x = ROUND_OFF(y,z)
|
- MIN function: x is assigned
minimum of y and z.
- MAX function: x is assigned
maximum of y and z.
- CEIL function: x is assigned
smallest integer not less than y.
- FLOOR function: x is assigned
largest integer not greater than y.
- ROUND_OFF function: x is assigned
z rounded to y significant digits (NOT y decimal places) with
trailing 0's truncated.
|
| Place an exact number of effector sites on defined regions |
| Version 2.53 May 28 2002 |
|
DEFINE_EFFECTOR_SITE_POSITIONS {
REGION existing_object_name[existing_region_name] {
EFFECTOR_STATE effector_state_name {
NUMBER = numerical_expression
POLE_ORIENTATION = orientation
}
...
}
...
} |
| By this function, you may place an exact number of effector sites on defined regions.
|
| Define Regions |
| Version 2.52 April 11 2002 |
|
DEFINE_SURFACE_REGIONS {
OBJECT existing_object_name {
REGION region_name {
ELEMENT_LIST = [element_specifier]
}
...
}
...
} |
|
Define surface regions on object templates, may define
regions for as many objects as desired.
Potentially pathological uses:
- Making a template object, defining a region on that object, placing effectors on that region;
- Making two copies of the template, adding a second region to one copy, placing effectors on both regions;
- Instantiating the two copies of the template.
|
| Place effector sites on defined regions |
| Version 2.52 April 11 2002 |
|
DEFINE_EFFECTOR_SITE_POSITIONS {
REGION existing_object_name[existing_region_name] {
EFFECTOR_STATE effector_state_name {
DENSITY = numerical_expression
POLE_ORIENTATION = orientation
}
...
}
...
} |
| By this function, the effector sites will be placed on
the defined regions based on its density.
|
| Volume dependent molecule release number |
| Version 2.52 March 29 2002 |
|
VOLUME_DEPENDENT_RELEASE_NUMBER {
MEAN_DIAMETER = c1
STANDARD_DEVIATION = c2
CONCENTRATION = c3
} |
| which will compute the number to release based upon a
fictitious mean vesicle diameter, standard deviation for the
diameter and filling concentration for the vesicle. The diameter
will be normally distributed but the vesicle volume and therefore
number in the vesicle will be non-normally distributed. Note that
the MEAN_DIAMETER parameter refers to a fictitious diameter and
has nothing to do with the SITE_DIAMETER parameter for the SPHERICAL_RELEASE_SITE.
|
| Gaussian distributed release number |
| Version 2.52 March 29 2002 |
|
GAUSSIAN_RELEASE_NUMBER {
MEAN_NUMBER = n1
STANDARD_DEVIATION = n2
} |
| This function will release a normally distributed number of molecules.
|
