Eppley Institute for Cancer Research

University of Nebraska Medical Center

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.prj File

What is it for?

The .prj file contains information about project settings, locations of files, and other information.  It is maintained by BEAM-ish and should not need to be edited by the user.

Who generates it?

BEAM-ish

Type?

Text

How is it formatted?

The .prj file follows the same format as a typical windows .ini file.  It has the following sections and parameters:

[General]  -  This section contains general information about project files and locations
projectpath  -  The path were the project files can be found
projectprefix - The prefix that is used to generate default files for a project
imagepath  -  The path were the images are stored
imageprefix  -  The image template where #### shows the part of the name that is variable
lastimage  -  The last image viewed when this project was open
crystalid  -  An integer that is used to identify the crystal the images were generated from
swapimagebytes  -  Used to determine if bytes were swapped or not.  This is no longer used.

[Mosflm]  -  This section contains information used to start MOSFLM
ScriptFile  -  The script file created by BEAM-ish to actually start MOSFLM
ImageToOpenOnStart  -  The image MOSFLM will open when it is started
mtzFile  -  The mtz file to use when starting HALFSLICE
beam_center_x_mm  -  The beam center in mm in MOSFLM coordinates
beam_center_y_mm  -  The beam center in mm in MOSFLM coordinates
crystal_to_detector  -  Crystal to Detector distance in mm
lambda_A  -  Wavelength in angstroms
Twotheta  -  Value of two theta
StartingPhi_Deg  -  Starting phi for the image (MOSFLM uses Image Header for Value)
DeltaPhi_Deg  -  Oscillation distance of images (MOSFLM uses Image Header for Value)
Gain  -  Gain value the (default seems to work fine)
VDiv  -  Vertical Beam Divergence (default seems to work fine)
HDiv  -  Horizontal Beam Divergence (default seems to work fine)
DetectorType  -  Detector Type (currently only ADSC by BEAM-ish)

[Halfslice]  -  This section contains information used to start HALFSLICE
InpFile  -  This file contains information about files and locations to aid in integration
Profile  -  This file contains the profiles calculated by HALFSLICE
PredictionFile  -  This file contains updated x y assignment after integration
HalfinFile  -  This file contains the h k l x y assignments for reflections that will be integrated
SigmaCutOff  -  This is used to limit the reflections assigned for profiling
FullWidth  -  This is the number of images the profile will span
StartImage  -  This is the image number to start at
EndImage  -  This is the image number to end at
MidAngle  -  This is the angle in the header of the image in the middle of the sequence

[Peakstats]  -  This section contains information that is used by PEAKSTATS
CNTRFile  -  The control file for PEAKSTATS
OutputFile  -  The is the file where PEAKSTATS writes the profile data
FWHMFile  -  This is the file where PEAKSTATS writes information about the reflection location and other data
FitFile  -  This is the file where information is stored about reflections that have Gaussian fits.
sigma_x  -  Beam divergence in the x direction
sigma_y  -  Beam divergence in the y direction
sigma_z  -  Spectral Divergence
mm_pixel_x  -  pixel x resolution
mm_pixel_y  -  pixel y resolution
AvgFilter  -  Use averaging filter 1(yes) 0(no)
AvgFilterWd  -  Width of the averaging filter in images
AvgIgnoreSelf  -  During averaging calculation ignore self 1(yes) 0(no)
PrntProfiles  -  Generate .dat2 after run is complete
AppDezinger  -  Apply dezinger filter 1(yes) 0(no)

[Gaussians]  -  This section contains information related to Gaussian fitting
DefaultNumberGaussians  -  When setting up a new fit the number of Gaussians to supply by default
DefaultBGType  -  Type of default background measurement (2)Linear (1)Constant 0(none) 
Metric#  -  Math mathematical representation of default parameter for Gaussians

[Filters]  -  This section contains information about the reflection filter parameters
Filter#  -  Filter information
AlwaysKeep  -  Comma separated list of Reflection Id's that should always be kept independent of filtering conditions
AlwaysDelete  -  Comma separated list of Reflection Id's that should always be filtered out independent of filtering conditions

[Colors]  -  This section contains information about the image color scheme
ColorSettings  -  Representation of the color scheme