nprocess: Automatically integrate multiple sets of images
The "nprocess" program was developed to automate the normal routine of
image processing in the Denzo-SMN GUI as much as possible.
Usage
The program is invoked by the command line:
nprocess [options] <pattern of kcdfilenames> [cellfilename]
If no "pattern of kcdfilenames" is present (or less than 2 files
match), all kcd files in the current directory are considered. Files
must be uncompressed KCD files.
A cellfilename, if any, is a ".x" file (the associated .kcd file must
exist as well) or a ".rmat" file containing an orientation matrix.
If not specified, one such file is taken from the current directory
as default.
To process images from a read-only medium like a CD, go to an empty
directory and type a command like "nprocess /cdrom/s*kcd", the ".x"
files will be created in the current directory.
Option that are recognized currently:
- gui
-
If this option is given, a window will be popped up that allows the
user to select the scans that need to be integrated. This is the
default if no kcd file names are given on the command line.
- nogui
-
If this option is given, no dialog windows will be popped up at
all, and the integration will run using defaults and command line
parameters only.
- norun
-
if specified, will inhibit the actual denzo run. In this
case "nprocess" will only prepare the denzo input files.
- mosaicity=m
-
Change the mosaicity (in degrees) to m.
- fixmosaicity
-
Fix the mosaicity during the denzo runs.
- fixdistance
-
Fix the crystal to detector distance during the denzo runs.
- spotradius=s
-
Change the spot radius (in mm) to s.
- backgroundring=s
-
Change the width of the background safety margin around peaks (in mm)
to s. Normally 0.1 mm.
- together=n
-
Change the number of images processed together to n.
- resolution=low,high
-
Change the resolution limits for integration to low,high.
- noxdisp
-
Inhibits the startup of the "xdisplayf" program.
Operation
If no image files were specified on the command line, or the
command line option GUI was specified, a list of scans shows up
on the screen:
Using the check buttons on the left, scans to be integrated can
be selected and scans to be left alone can be deselected.
To perform the integration, the program needs a single ".x"/".kcd"
file combination or a ".rmat" file to get the orientation matrix of
the crystal on the diffractometer. A window similar to the one used
in "collect" will pop up to get these cell parameters (see the chapter on datacollection in the
collect manuals).
A number of denzo parameters is also retrieved from the ".x" file
specified (or from the command line), and presented in a final dialog:
- Lower resolution
-
The lowest resolution at which data should be integrated. On a
KappaCCD, if the smallest beam stop is used and the beam stop is as
close to the crystal as it can be, all reflections with a resolution
lower than 7 angstrom are (partially) occluded. If the beam stop is
pulled out a bit, this number raises quickly.
- Upper resolution
-
The highest resolution at which spots might be observed. A 27.5 degree
data collection using Mo-Ka radiation is 0.79 Angstrom resolution.
- Spot radius
-
Gives the radius (in mm) of the diffraction spots as they should be
integrated. If the "findresolution" program has been run, the default
is probably reasonable. If spots become red in the display window
during the integration because they are overlapping, you could try to
reduce this value.
- Background ring
-
Gives the width (in mm) of the safety ring around reflections.
It is normally chosen to be 0.1 mm.
- Mosaicity
-
Gives the initial mosaicity (in degrees) where "denzo" will start the
refinement.
- Space group name
-
The name of the space group used to define which of the 6 cell parameters
are tied together or fixed.
- Process together
-
-
The number of frames "denzo" should integrate as a single batch. The
default is calculated from the rotation angle per frame used in the
measurement, such that the frames that are processed together form
about 15 degrees of data (for small molecules that should be
fine). The exact value used for each data set may vary a bit, because
it will try to avoid "leftovers" at the end of a set (imagine a 41
frame set with a "process together 10", it will leave the last single
image which might contain insufficient reflections to refine the unit
cell).
Under "more options", we find a few more options:
- Wavelength
-
The wavelength at which the experiment has been performed. Should probably
not be changed.
- Primary beam X and Primary beam Y
-
The primary beam position in the screen (around 30,30 mmfor a 65mm
KappaCCD). The defaults are taken either from the .x file used to
obtain the unit cell, or from the calibration file (def.site).
Should never require changes.
- Fix mosaicity
-
If "yes" is selected here, "denzo" will be instructed not to refine
the mosaicity. Therefore the "initial mosaicity" specified above
will remain.
Once the parameter window is closed by "OK", the program will create a
number of denzo scripts in the current directory, and start running
the integration (unless this is inhibited by specifying the "norun"
option on the command line).
The actual integration will first pop up an "xdisp" program. If you
activate "update predictions", you will be able to follow the
integration process and see whether the cell is properly refined. Log
files from "denzo" will be left in denzo*.log.
When the integration is completed, a window will pop up
showing some parameters that are refined by denzo, together with
a "quick judgment" whether the parameter and/or its variation over
the integration looks OK.
If you need to change a denzo parameter to change the integration,
chances are that you can find it in the file "denzosetup.cmd" and
change it with a text editor. You can then re-run denzo manually
from the command line, using the appropriate .cmd file as input. e.g.:
denzo < denzos01f.cmd
