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Configuration of the Collect programs

1. a file /usr/local/lib/nonius-config.py
2. a file .nonius-config in your home directory (Please note the initial "." character, which renders this file invisible for the normal "ls" command).
3. a file nonius-config in your current directory, or if that one does not exist, in the directory one up from the current directory.

You should put a parameter in (1) if it should be the system default for all users; put it in (2) if it is your own default, but other people might want to use other values; put it in (3) if it is only required for a single project.

The configuration files are read as "python" programs, and therefore syntax is very important. The best way to use it is to only use variable assignments or function calls, like described below. If required, you can comment out lines from your configuration file by preceding them with a '#' character.

Note:

• Leading space is significant. Start all assignments in the first column.
• Variable names are case sensitive.

Functionality groups

Due to the "default-like" nature of these function calls, they should probably be used only in the site-wide configuration files, and even there only at the beginning [but this is not enforced].

The available functions are:

default_protein()

This switches from the default "small molecule" parameters to more protein-like parameters. At this time, the following parameters are set:

 
resomode=1
minscanserieslength=2
processtogether=2
maximumhighresolution=8.0
indexscanrange=2.5
indexframeangle=0.5
indexdegreetime=60
resolution=2.5
indexdx=60
completeness=0.98
chiralonly=1
resolutioncircleradius=(10,5,4,3,2)
peaksearchthetamin=1.5
defaultwavelength=1.541838

default_eval()

This switches from the default denzo/scalepack setup to evalccd. At this time, the following parameters are set:

eval14_installed=1
dirax_installed=1
sadabs_installed=1 # But ONLY on Linux systems!
superguidata='eval14'
superguiindex='phichi'
dxfactor=1.4
autodark=1

default_noprotein()

Changes all parameters set by default_protein() back to their default values that are more suitable for small molecule work. This can be useful to determine a single small molecule structure in a predominantly protein environment.

default_denzo()

Changes the parameters set in a "mostly eval14" shop back to values suitable to working with denzo. This is the 'opposite' of default_eval().

Scan parameters for when nothing is known about the crystal

indexscanrange

The parameter "indexscanrange" can be used to change the default scan length for a cell determination scan. For a phi/chi scan, the phi-range used is half of this value. This number is also used by the "prescan" program. Value is in degrees.

indexframeangle

The "indexframeangle" is the default frame angle proposed for index scans by "collect". In degrees.

indexdegreetime

The default exposure time proposed for index scans by "collect". In seconds per degree.

phichiaddheightscan

Add an extra phi scan at large chi offset to the phi/chi strategy to be able to determine the "height" of the crystal in a refinement cycle.

phichiexposuretime

The default exposure time for phi/chi scan frames used by "collect" and by "prescan". In seconds per exposure.

indexstrategy

Chooses the strategy for index scans proposed as default by "collect". It should be set to the position in the presented list of strategies, the first one being 0.

indexdx

default crystal to detector distance for cell determinations (mm)

indextheta

default detector theta angle for cell determinations (degrees)

datcoldx

default crystal to detector distance for data collections (mm). This value is only used if nothing is known about the crystal when the data collection is initiated.

Defaults:

indexscanrange=10
indexframeangle=1
indexdegreetime=20
phichiexposuretime=60
indexstrategy=0
indexdx=40
datcoldx=35

Peak searching

initialpeaksize

Initial peak size used by the accurate peak integration algorithm. Do not touch except when told to touch.

maxpeaksize

Maximal peak size accepted by the accurate peak integration algorithm. Do not touch except when told to touch.

maxpeaksearchratio and maxpeaksizedifference

Often, very asymmetric peaks are artifacts and should not be considered. At peak search time, peaks that have a horizontal to vertical size ratio that exceeds the maxpeaksearchratio (default 2.5) and for which the difference in size is more than the number of pixels given in maxpeaksizedifference (default 4) will be rejected.

maxpeaksearchsize and minpeaksearchsize

When looking for peaks, the horizontal and vertical sizes measured in pixels must be between these two values. The default minimum is 2 pixels, that way most of the zingers or warm pixels that would otherwise come through will be rejected at this stage. If the maximum is set too high, a large fraction of the image could be recognized as one peak if there is low-angle background scattering. The default value of 40 should only be raised if there are seriously larger peaks to be considered.

peaksearchthetamin

The lowest theta at which peaks for rotindex will be accepted.

peaksizefraction

The 'peak integration' routine in collect uses this number to estimate the break-off limit between peak and background area's. In normal cases, 0.7 is a good value. However, if you want to look specifically at the spot radius of strong reflections, 0.5 may suit better.

usepeakdb

If set to 1, the peak search routine will look in a peak database first. This peak database will be editable using ndisp later, but for now this is just a time-saver if you do multiple peak searches on the same data.

initialpeaksize=4
maxpeaksearchratio=2.5
maxpeaksearchsize=40
maxpeaksize=10
maxpeaksizedifference=4
minpeaksearchsize=2
peaksearchthetamin=4
peaksizefraction=0.7
usepeakdb=1

GUI presentation

bgpossible and bgpossiblehigh

Colors used for buttons when they can be used.

bgimpossible and bgimpossiblehigh

Colors used for buttons when they can not be used.

bgtodo and bgtodohigh

Colors used for buttons when their action has not been completed.

bgdone and bgdonehigh

Colors used for buttons when their action has been completed.

bgok

Color used for message windows indicating success

bgwarning

Color used for message windows indicating a warning

bgerror

Color used for message windows indicating an error situation

bgbusy

Color used to indicate an "active" process.

bgframe

Color used by some rectangular areas in the gui to set them apart from the rest.

bgcolors

In case you are running multiple projects simultaneously, the background color of the complete GUI will be different for each project. The colors that are used, in order, are taken from the bgcolors list.

Color names are given in the standard X-window methods (look in the file "rgb.txt" that comes with your system to get some ideas for color names).

fontsize

Adapts the font size used in the GUI programs to the screen size, eye quality, and the size of the audience.

initialballoonhelp

The initial state of the "balloon help" can be "on" (1) or "off" (0).

autoiconifysupergui

If set to 1, reduces screen clutter by iconifying supergui during long lasting operations (e.g. data collection or integration).

autoiconifycollect

If set to 1, reduces screen clutter by iconifying the main collect window during the data collection.

iconifyevalmessages

If set to 1, reduces screen clutter by iconifying the raw text output from the eval program in makextalevc.

bgpossible='springgreen2'
bgpossiblehigh='springgreen1'
bgimpossible='indianred2'
bgimpossiblehigh='indianred1'
bgtodo='indianred2'
bgtodohigh='indianred1'
bgdone='springgreen2'
bgdonehigh='springgreen1'
bgok='springgreen2'
bgwarning='yellow2'
bgerror='indianred2'
bgbusy='yellow2'
bgframe='grey60'
bgcolors=["grey85","#DFF","#DDF","#FDF","#FDD","#FFD","#DFD"]
fontsize=12
initialballoonhelp=0
autoiconifysupergui=0
autoiconifycollect=0
iconifyevalmessages=0

hidecsd

Hide the options that can look for unit cells in the Cambridge Structural Database.

hidepowder

Hide the options that can deal with powder samples.

hidetwin

Hide the options that are tailored for dealing with twinned samples.

hidemodulated

Hide the options that can deal with modulated samples.

hidecsd=0
hidepowder=0
hidetwin=0
hidemodulated=0

Error condition handling

crashinvalidhkl

If enabled programs that read a shelx.hkl style file with an invalid intensity (typically '********') will stop. If disabled, they will continue after printing an error message and throwing out the invalid reflection.

Defaults:

crashinvalidhkl=1

Support for other software

denzo_installed

Indicates whether "denzo" is installed on the system. If this is set to 0, you will need the "dirax" and "evalccd" packages for supergui to work.

denzo_program, scalepack_program and xdisp_program

If more than one version of the HKL programs are installed on the system, these parameters can be changed to make the "collect" programs call the proper version. It can also be used to indicate the location of the HKL programs when they are not in your PATH.

denzoneedsextratogether

If this is set to 1, an extra "process together" command is inserted into the denzo command stream, apparently working around a problem where denzo would process a proper batch of frames together first, but the rest of the frames would be processed one-by-one.

dirax_installed

Indicates whether dirax is installed on the system.

dirax_program

Where to find dirax if there is more than one version, or if it is not installed in your PATH.

sadabs_installed

Indicates whether sadabs is installed on the system. A sadabs executable comes with the Linux version of evalccd.

sadabs_program

Hard-coded location of the program.

sadabs_terminal

The sadabs program is a command line program. This parameter specifies how supergui should create a terminal to execute sadabs.

eval14_installed

Indicates whether evalccd and the other eval-associated programs are installed on the system. Please note that even if you are using eval only in selected projects, you must enable this variable either in your home directory configuration file, or in the system wide configuration file as well.

eval14_program

Hard-coded location of the program.

pixel15_installed

Indicates whether pixel15 and the other eval-associated programs are installed on the system. Pixel15 is a profile-predicting successor to eval14.

pixel15_program

Hard-coded location of the program.

platon_installed

Indicates whether platon is installed on the system.

solve_installed

Indicates whether the Solve program is installed on the system.

maxus_installed

Indicates whether maXus is installed on the system. If this is set to 0, you need "platon" for supergui to work.

x2sad_installed

Indicates whether x2sad is installed on the system. x2sad is a program from the shelx-suite that can be used to prepare denzo .x files into a sadabs input file. Denzo/collect users can license x2sad and sadabs separately.

x2sad_program

Hard-coded location of the program.

Defaults:

denzo_installed=1
denzo_program="denzo"
denzoneedsextratogether=0
scalepack_program="scalepack"
xdisp_program="xdisp"
dirax_installed=0
dirax_program="dirax"
sadabs_installed=0
sadabs_program="/usr/local/nonius/utrecht/sadabs/sadabs"
sadabs_terminal=["xterm","-e"]
eval14_installed=0
eval14_program="/usr/local/nonius/utrecht/ccd/evalccd/evalccd"
view_program=None
platon_installed=0
maxus_installed=1
pixel15_installed=0
pixel15_program='../utrecht/ccd/pixel15/pixel15'

EvalCCD integration defaults

norotshift

If this is set to 1 (the default), makextalevc will write xtal.evc files that tell eval that the predicted rotational position of a reflection is more accurate than the individually refined value. This should probably stay at the default except if you are using finely sliced data.

shoedepth

The default thickness of the shoe boxes (in frames) used by "makeshoe".

shoesize

The default size of the shoe boxes (in pixels) used by "makeshoe".

shoemakepreref

Enable/disable the cell prerefinement feature of makeshoe by default.

shoemakelow

Enable/disable the makelow feature of makeshoe by default.

someplotbatch

How often to show a frame during shoe box generation if the "Some" option is selected (once every "someplotbatch" frames the frame is drawn).

Defaults:

norotshift=1
shoedepth=5
shoesize=21
shoemakepreref=0
shoemakelow=0
someplotbatch=10

Cambridge Structural Database searches

csdaxiscrit

The relative deviation allowed to each of the unit cell axes in the CSD query. This can normally be left at 0.015 (1.5% deviation).

csdhome

The location of the csd. This is either a directory on the local machine (i.e. '/usr/local/csd' or '/opt/cambridge') or a host name, followed by a ":" and a directory on a remote server (i.e. 'csdserv:/usr/local/csd' or 'pc101:/opt/cambridge'). If the latter option is chosen, an "rsh" command to the remote server must be allowed. This variable must be configured for the CSD options in collect to function

csdmatrixcrit

The relative deviation between the final axis matrix of the hit and the axis matrix of the query unit cell. If you get too many false hits, reduce this number by a factor of 2.

csdprog and csdconquest

The name of the command-line query program and the conquest program. These should normally not require changes.

csdrsh

The name of the "remote shell" program used to access a database running on a remote computer. This can be either "rsh" (the default), or "ssh". For some versions of "ssh", the "csdhome" variable can also be set to "user@host:/directory" to specify that the database query should be run as another user. But: ssh should not ask for a password, otherwise programs may hang forever.

csdrshluser

The remote username in case the "rsh" program does not understand the "user@host" syntax. If this is set to a non-empty value, the "-l username" parameters are passed to the csdrsh program.

csdbases

A space separated list of databases to query. The word "Master" identifies the CSD master data base. Example:

  csdbases="/home/my/localcsd /home/collaborator/localcsd Master"

csdvolumecrit

The relative deviation allowed to the cell volume in the CSD query. This can normally be left at 0.03 (3% deviation).

Defaults:

csdaxiscrit=0.015
csdconquest='cq'
csdhome=None
csdmatrixcrit=0.05
csdprog='squest'
csdrsh='rsh'
csdrshluser=None
csdvolumecrit=0.03

CD and DVD writing

cdwriterdev

This gives the SCSI device name for the CD writer. this should be a string consisting of 2 or 3 numbers separated by a comma. If you have one scsi interface, it is "scsi id,scsi lun". If you have more than one scsi interface it is "scsi interface,scsi id,scsi lun". The "scsi lun" should most probably be 0. Example: "4,0". Making a typo here could destroy your system disk. Make sure you do it right. Also note that the value should be enclosed in quotes (it needs to be a string).

cdwriterimage

This is a file where a temporary copy can be made of the contents of the CD/ROM. This might need up to 700MB of free space.

cdwriterlog

This is a summary file where all your CD writing activities will be logged for later reference.

cdwriterspeed

This is the speed multiplier factor for your CD Writer. By default, CD's will be written at "single speed", which may take up to 74 minutes for a full CD. Many CD writers nowadays are able to write at quad speed. If you own such a device, you can set "cdwriterspeed=4". Please note that rewriteable media can not be written at very high speeds, so if you plan to use rewriteable CD/RW disks, be conservative when setting this configuration parameter.

dvdwriterdev

The device file for your DVD writer. This is often "/dev/dvd". If this variable is set, all "cd" variables above are ignored, and DVDs are burnt with help of the program growisofs (which must be installed from another source).

growisofsoptions

This is a list of options to be passed to growisofs when writing a DVD image.

cdwriterdev=None
cdwriterimage="~/cdrom.img"
cdwriterlog="~/cdrecord.log"
cdwriterspeed=None
dvdwriterdev=None
growisofsoptions=['-R','-J']

Files and file names

communicationlog

Name of the file where all communications with the server PC are stored for later perusal. If "communicationlogfile=None", the communications are not stored at all (which will make it a lot more difficult for us to trace a problem if it arises!)

eventlog

Name of a structured file where "special events" in the data collection process are noted down including a time stamp. Can be suppressed by setting "eventlogfile=None". This does not contain everything you might want. If you feel something is missing, please let us know at collect@bruker-axs.nl

hashfilepattern

By default the names of images measured for a data collection start with the letter 's' or 't' etc, and for a cell determination with the letter 'i' or 'j' etc. The rest of the filename is determined by the filename pattern given in the parameter 'hashfilepattern'. If you expect to make regularly more than 100 scans or more than 1000 images per scan using "collect", this is the parameter to change.

rpclogfile

The file where the "xml-rpc" server (if used at all, for it is still optional at this time (4/2000) will log all actions. This must be a valid filename, it can not be set to None.

interactlog

The file where interactions with fortran programs from the evalccd package and with dirax are logged. If this is set to None, the interaction will not be logged.

communicationlog='communication.log'
eventlog='nonius.log'
hashfilepattern='##f####.kcd'
rpclogfile='/dev/null'
interactlog='interact.log'

Hardware connection

ccdhostname

The name of the default KappaCCD server PC.

Unlike most other configuration parameters, this parameter can be overwritten by setting an environment variable CCD_HOSTNAME in the shell. This is only for backward compatibility, and use of this environment variable is discouraged.

Before this configuration variable was available, all systems were installed with the CCD_HOSTNAME environment variable. Since it is more flexible to set the configuration parameter than to use the environment variable, it is better to remove the environment variable from your .cshrc file, and add the configuration parameter to your configuration file.

defaulthardwaretype

The type of hardware driver is normally the "KappaCCD Server connection", but there are a few alternatives. The default can be set using this variable. It should be set to an integer number that points to the sequence number of the desired driver in the hardware device list that pops up when you select the hardware type. The first item is numbered 0.

ccdhostname="no202"
defaulthardwaretype=0

Things to do during data collection

displayduringcollect

If set to 1, the "collect" program will display the collected images during data collection.

Please note that the ndisp program will only be started once. If it is "quit"ted, no more images will be shown. ndisp can be started in slave mode to resume image display.

progressfile

The name of a file to write the contents of the "yellow progress window" of the collect program to. If set to the empty string (the default), the text is not written to a file. This can be used to monitor a data collection from a remote place.

xtalsnapinterval

Another thing that can be done during data collection is to regularly take snapshots of the crystal, and save these snapshots in a special subdirectory. This variable sets the minimal number of seconds between these snapshots.

xtalsnapdir

Specifies the name of the subdirectory where the snapshots are stored

xtalsnapformat

Specifies 2 strings: the filename extension of the snapshot files, and the file type. All file types supported by the Python Image Library (PIL) are supported here.

displayduringcollect=1
progressfile=''
xtalsnapinterval=60*60
xtalsnapdir="xtalsnap"
xtalsnapformat=(".ppm","PPM")

Mouse sensitivity in 3D windows

mouserotspeed

Specifies how fast the model should rotate if the mouse is dragged with button 1 pressed.

mousescalefactor

Specifies how the model is scaled for every pixel the mouse is dragged with button 3 pressed.

mouserotspeed=0.01
mousescalefactor=1.003

Server options

servertemperaturecheck

Can be set to 0 to disable the detector temperature check performed before each measurement on the server. This is a very bad idea. If there are problems to reach -60C, and you really need to perform measurements before this problem is solved, you should set the detector temperature a few degrees higher, not use this option.

serverdezinger

Can be set to 1 to enable server-side dezingering of images. This is a bad idea since it will upset some of the calibrations, and the server can only dezinger 2-fold images.

servertemperaturecheck=1
serverdezinger=0

Generator power

nominalvoltage

A dictionary describing the preferred voltage to use for each target material. The target material should be given as all capitals, the voltage as an integer in kV. If the nominal voltage for the active tube is not mentioned in the list, approximately 2.5 times the critical voltage will be used.

nominalpowerfraction

The fraction of the maximal current that will be used. At 1.0 (100% of rated power) the tube lifetime is significantly shorter than at the default 0.9.

lowvoltage

If positive, the "idle" voltage (in kV) for the generator. If negative, it tells the collect programs to turn the voltage down by that amount from the standard operational conditions (in this case a minimum of 20kV is enforced).

lowcurrent

If positive, the "idle" current (in mA) for the generator. If negative, it tells the collect programs to turn the current down by that amount from the standard operational conditions (in this case a minimum of 5mA is enforced).

minimalpowerfraction

The minimal fraction of the maximally allowed current (mA) that is still considered a reasonable power for the generator to perform measurements. If the current is lower than this, many of the auxiliary programs in the collect suite will decide to turn up the power automatically.

nominalvoltage={'MO':60,'CU':45,'AG':60}
nominalpowerfraction=0.9
minimalpowerfraction=0.50
lowvoltage=-15
lowcurrent=5

Cryostat defaults

lowtemperature

The default low temperature (in K) presented by "collect"

temperaturerampspeed

The speed at which the crystal temperature should be changed (in K/hour) if no explicit value is specified. If a value larger than 360 is specified, a model 700 cryostat from Oxford Cryostat will be instructed to "COOL" as quickly as possible instead.

coolerlowkappa and coolerhighkappa

Used to configure the "Low temperature limitations" in the collect strategies. These two parameters are limiting the absolute value of the kappa position to ensure a laminar flow of conditioned Nitrogen gas. Most useful if the cryostat is mounted nearly vertical.

cryolimit

The temperature (in K) below which a measurement is considered to be "cryogenic". If the temperature is set below this value, the goniostat will be moved regularly when idle, and defaults of programs may be adapted.

cryolimitkappa

If this is set to 1, the "low temperature kappa limitations" will be enabled by default when "collect" sees you are using cryogenic conditions.

alwayscryowait

If this is set to 1 (the default) all shutter-open scans will always wait for the cryostat to finish a temperature change.

cryophiscanchi

The chi angle (degrees) at which a phi scan can be made to avoid the cold stream. If this is lower than the equivalent of "coolerlowkappa", no phi scan will be made when the low temperature kappa limitations are in effect. This is also used by the "phi/chi" scan procedure.

temperaturetolerance

If the "actual temperature" stored in the image header differs by more than this tolerance from the current "setpoint temperature", a new click on the "Collect data" button in collect will recollect the image.

lowtemperature=150
temperaturerampspeed=240
coolerlowkappa=15.0
coolerhighkappa=120.0
alwayscryowait=1
cryolimit=273
cryolimitkappa=1
temperaturetolerance=0.5
cryophiscanchi=19

Beam stop parameters

beamcatcheraccuracy

Defines the maximal positional error of the crystal and the beam stop (in mm).

beamcatcherbladethickness

The thickness of the blade supporting the beam stop (in mm). This is always 0.5 mm.

beamcatchercrystalsize

The approximate largest diameter of the crystal. If this is set to "None", the diameter of the crystal is calculated as a quarter of the size of the beamstop. This corresponds approximately to the diameters of the collimators used on a KappaCCD.

beamcatcherdiameter

The default beam catcher diameter (the three beam catchers that are delivered with the KappaCCD are 1.0, 1.5 and 2.0 mm). This value is only used if there is no value in the header, or if the "beamcatcherheaderreliable" parameter is set to 0.

beamcatcherdistance

The default beam catcher distance (the distance between the crystal and the front of the beam catcher. At dx=25, this is normally around 6 mm). This value is only used if there is no value in the header, or if the "beamcatcherheaderreliable" parameter is set to 0.

beamcatcherheaderreliable

If this is set to 0, the beam catcher values in the KappaCCD header will be overwritten.

beamstopwidth and beamstoptau

The width (mm) and angular orientation (degrees) of the beam stop image. These parameters are used by makeshoe to mask out the blocked area of the detector. The actual values are dictionaries with the detector ID as key. If no value is given for the specific detector ID, the value for '*' is used instead. These parameters might be calculated from the above parameters in the future.

beamcatcheraccuracy=0.2
beamcatcherbladethickness=0.5
beamcatchercrystalsize=None
beamcatcherdiameter=None
beamcatcherdistance=None
beamcatcherheaderreliable=1
beamstopwidth={'*':1.5}
beamstoptau={'*':0.0}

Scan redundancy

redundancyfactor

This is the default redundancy that will be asked for in "collect". If it is larger than 1, a "redundant" strategy will be calculated by default.

redundancyfraction

This determines what fraction of the dataset should have at least the desired redundancy. See the page on redundancy for details.

redundancyreportvalues

In reports about the redundancy of a data set, a list of redundancies at different percentiles is printed. Which percentiles are printed is determined by this parameter.

redundancyfactor=1.0
redundancyfraction=0.9
redundancyreportvalues=(0.01,0.10,0.50,0.90,0.99)

SuperGUI parameters

superguimode

Used to initialize the mode of operation of supergui. It can be set to one of these values:

• 0 = Manually
• 1 = Automatically
• 2 = Automatically from data collection onwards

superguiindex

Tells "supergui" which method you prefer for indexing. Valid values are "denzo" and "phichi". This variable is only used if you have both denzo and dirax installed on your system.

superguidata

Tells "supergui" which method you prefer for integration. Valid values are "nprocess", "denzosmn", "x2sad" for different ways of using the HKL programs, and "eval14".

superguiprescanbutton

If set to 1, tells supergui to include a "PreScan" button before the "Index" button.

superguisolve

Tells "supergui" which method you prefer for solving structures. Valid values are "maxus", "platon" and "solve". This variable is only used if you have more than one of these programs installed on your system.

xtalbasedir

Tells supergui where collected data are generally stored. This is used to prompt for the directory to open projects.

xtaloperators

Either a list of "operator" names, or a dictionary associating operators with their working directories.

If xtaloperators is a list, this is used to construct the first element of the directorypath to the measurement data. Oops, that sounds confusing, lets make an example: In Delft, we have

xtaloperators=["bram","anita","leo","rob"]
xtalbasedir="/diska"

Now if "rob" wants to measure a crystal named "xtal1", the chosen directory is "/diska/rob/xtal1".

Alternatively, we could have specified the same directory layout as:

xtaloperators={"bram":"/diska/bram",
               "anita":"/diska/anita",
               "leo":"/diska/leo",
               "rob":"/diska/rob"}

This last form is more flexible: it allows you to have different operators that are using completely different areas on the disk.

Defaults:

superguimode=1
superguiindex=None
superguidata=None
superguisolve=None
xtalbasedir=None
xtaloperators=[]

Display parameters

maxdisplaysize

If an image that is read is larger than this parameter, the "ndisp" program will 'bin' the image before displaying it. Binning is performed until the image is smaller than the maxdisplaysize. If "maxdisplaysize" is an integer (e.g. 700), the image will be scaled down by an integer factor. If "maxdisplaysize" is a floating point number (e.g. 700.0), the image will be scaled to exactly this size.

raisedisplay

Setting this to 1 makes sure that whenever the "ndisp" program loads a new image, it raises itself on top of all other windows on the screen.

profilecsv

If this parameter is set to 1, each "general profile" created in ndisp will write the profile to a comma separated value file for external processing. The output file for this option is ndisp-profile.csv

displayfullscale

The scaling maximum (i.e. the intensity that corresponds to "white", with 0 corresponding to "black") used by the default "fixed contrast" mode in ndisp.

displayextras

If this is set to 1, which is the default, the program will start up with the buttons on the side and the statuslines at the bottom. If set to 0, these will be missing when the program starts. Possibly useful during live presentations.

displayscaletype

The default scaling type. Should be either "log" or "linear".

displaycolorscheme

The default color scheme used by ndisp. A number.

• 0: white spots on a black background
• 1: black spots on a white background
• 2: white on black with red for very high and blue for very low values.
• 3: color scheme 1
• 4: color scheme 2

This is the same order as the color schemes mentioned in the "Options" menu of the "ndisp" program.

maxdisplaysize=700
raisedisplay=0
displayfullscale=1000
displayscaletype='log'
displaycolorscheme=0
profilecsv=0

The names and default values for these are:

adcfilter=1
airabsorptionfilter=0
badpixelfilter=1
darkfilter=1
incidencefilter=0
localdarkfilter=1
sensitivityfilter=0
shortdarkfilter=1

ndisppeakfiletool=0
ndispmousemirrortool=0

Parameters for evalccd

focusdistance

The distance from the tube focus to the sample, in mm (default 220; valid for a KappaCCD on a sealed tube). This is used by Evalccd for its ray-tracing algorithm.

focussize

The size of the tube focus, in mm (default 0.4; valid for a KappaCCD on a sealed tube). This is used by Evalccd for its ray-tracing algorithm.

maxfocussize

The maximal size of the X-ray focus, in mm. The default of 1.0 corresponds to a normal focus X-ray tube. Only raise this number if you are dealing with huge beam sizes on special instruments.

maxshoedepth

The largest number of frames allowed in a shoe box. The evalccd program has a compiled-in default of 31, but the gui limits this to 19 which should suffice for all practical purposes. Increase this variable if your purpose does not fit this.

maxshoesize

The largest number of pixels on an edge for a shoe box. The evalccd program has a compiled-in default of 61, but the gui limits this to 41 which should suffice for all practical purposes. Increase this variable if your purpose does not fit this.

xtaldiameter

The default crystal diameter in mm used by the "makextalevc" program if nothing else is known about the crystal size and shape.

focusdistance=220
focussize=0.4
maxfocussize=1.0
maxshoedepth=19
masshoesize=41
xtaldiameter=0.3

Other parameters

acceptdenzosign

When the "cifin" program is run on a non-centrosymmetric data set, it will try to find out whether the version of denzo you are using is inverting the absolute configuration of the data set. It will then present a confirmation dialog box, where you have to agree with the findings before the conversion can be commenced.

Using the acceptdenzosign parameter this dialog box can be suppressed. If "acceptdenzosign" is set to 1, the box will not be presented if the sign of the denzo data set is correct. If it is set to -1, the box will not be presented if the sign of the denzo data set is inverted.

If the variable is set to 2, this means that you are sure that the sign of the data is correct, and the test will be suppressed. Similar for -2, where you tell the collect programs that you are sure that the sign is opposite. The -2 value is strongly discouraged, and the 2 value should only be used on a system where no .x files from before HKL2000 will ever be reprocessed.

If this variable is set >0, it will also enable all HKL2000 compatibility flags.

anglemargin

Run-out angle at scan edges (degrees) ; i.e. the part at the beginning and at the end of each scan that is not used for prediction of reflections, to allow for crystal slippage and mosaicity.

anyexpert

Set this to 1 if you know all of the intrinsics of the any program. In that case the "nanny" program will show a command line.

autochiralpointgroup

If set to 1, the default pointgroup as determined from the crystal system will always be a chiral point group (i.e. suitable for a protein). This will result in a default strategy that collects Friedel pairs. If set to 0 (the standard value), the default pointgroup will be the lowest laue group compatible with the crystal system.

autoconnect

If set to 0, collect will always ask for confirmation before making a connection to the hardware.

autodark

There are different methods of correcting for dark current accumulation in the CCD. The "collect" package itself corrects for dark current using a short exposure shutter closed image and a long exposure shutter closed image (See chapter on dark current correction). Both of these images are made only during detector calibration. This assumes that the dark current is a fixed property of the detector.

The newest versions of the "denzo" and "evalccd" integration programs assume that the dark current can change over the lifetime of the detector, and so they prefer to have a shutter closed image measured under exactly the same conditions as every scan.

This is supported by "collect" using the "autodark" parameter. If "autodark=1", every scan of more than one image made by the collect program will automatically be finished by a shutter closed image of the same exposure time.

axcrit

Makes "collect" use a more efficient, experimental data collection strategy.

autostartserver

If set, makes all programs automatically start the rpc-master program if required.

axcrit

The default criterion used for Y. Le Page's algorithm for cell normalization. In degrees (It is not exactly the maximal accepted "deviation from 90", but that is how it feels).

backgroundradius

Background radius used in denzo runs from the GUI. Default of 0 means to make a reasonable default based on spots that were seen on some images.

backgroundradius

Background radius used in denzo runs from the GUI. Default of 0 means to make a reasonable default based on spots that were seen on some images.

cellaskkcdfilename

If this is set to 1, GUI programs will ask for both a .x and a .kcd file name to retrieve a unit cell. Use this if you regularly store .x files in a different directory from the .kcd file.

cellrefinedetector

The number of cycles of refinement of the detector positions performed by the phichi and rotindex program. Should be 0 or 1.

chiralonly

If this is set to "1", only chiral pointgroups and lauegroups will be presented.

cifinoutput

The name of the default output file for the "cifin" program.

ciftype

This string should be either 'maxus' or 'skb'. If it is set to 'skb', the cifin program will spend some more time filling in more CIF fields.

completeness

default target completeness for data collection strategies

defaultdatacollectionstrategy

Selects which data collection strategy is presented by default. This should be a number giving the position of the desired strategy in the list of possible strategies that is presented (0=first!)

defaultwavelength

Last resort if a program can not figure out which wavelength has been used for an experiment. Will probably never be used.

denzoindexcesd

If this parameter is set to 1, the "denzoindex" program will run "scalepack" to determine the estimated standard deviations on the unit cell parameters; if set to 0 this calculation is skipped.

detectorsizemargin

Dimensions of the edge of the detector that is not used for prediction of reflections, to allow for distortion and round-off.

dxfactor

this is multiplied by the longest unit-cell axis to get the minimum feasible 'dx' value for data collection. Reasonable values are 1.0 (very small spotsize) and 1.2 (normal spotsize), both assuming MoKa radiation. For other radiation types, the value is multiplied by the change in wavelength to compensate.

dxlimit

The longest DX arm to be expected on any machine. Default=300 mm, do not change this unless you have a dx arm that is longer than 300 mm.

exposuretimetable

For the table in findresolution, a number of predefined exposure times are defined in the configuration file. The exposure times given here will also preferentially be suggested times by datacollection in collect. Values must be numbers, in increasing order, separated by commas. The list should be surrounded by square brackets.

gamma

If no corrections for non-linearity of intensities are made, one can see much less differences between grades of black than between grades of white on a monitor. This can be solved using "gamma correction". The value of this correction can be changed here. A value of 1.0 means no correction. Normal values are between 1.4 and 2.5, depending on the monitor (not only brand and type, but also specimen). Using the program "testgamma", you can determine a reasonable gamma value of your monitor. You will have to judge by yourself whether that results in the best possible images in ndisp.

generatorcheckdx, generatorcheckpixels and generatorcheckzingers

For a generator stability check script, these are three parameters that determine the default distance to perform the measurement, the minimum number of pixels to be accepted as a reasonable stability measurement, and whether an attempt should be made to detect zinger pixels. Do not touch these unless you have been told so from Delft.

gonzeroaction

Indicates what to do when the goniostat asks to be restarted.

• A value of 0 means stop the program immediately.
• A value of 1 will mean "ask the user what to do", but has not yet been implemented.
• A value of 9 means "unconditionally issue a GONZERO command".

imageextension

This sets the default image extension used by some programs.

iboxsize

This sets the box size for the background box in denzo integrations.

inhibitgc

This flag disables the "garbage collection" option available in python 2.0. Do not touch except when told otherwise.

kcddatatype

By default the KCD file consists of a header followed by raw 16-bit unsigned data. This is called the 'u16' datatype. Alternatively the 'ccp4w' datatype can be used, which will store images in compressed form using compression routines from the CCP4 suite.

If the kcddatatype variable is set to None, the data will always be written in the form it was received. If it is set to either 'u16' or 'ccp4w', KCD images will always be converted to the desired type.

Currently the compressed images can only be read by the collect programs; hence the usability of this functionality is quite limited.

licensewarning

The number of days ahead of time that the licensing system will warn you of a pending expire.

localcifdata

This can be set to a character string describing some experimental setup parameters for the CIF output of cifin. This should be used for parameters that do never change between experiments performed at your site, but which are difficult to determine from the ".sca" file which is input into cifin. An example:

localcifdata='''
_diffrn_source_type  'Nonius FR590 Sealed Tube Generator'
_diffrn_radiation_source               'fine focus sealed tube'
'''

mailrecipient

The default recipient for E-mail sent by the collect program.

manualhkllimits

If this parameter is set to 1, collect will ask for additional h,k,l limits for applying to the data set. This makes it possible to measure limited parts of the Ewald sphere more efficiently.

maximumhighresolution and minimumlowresolution

Normal resolution limits for a small molecule data collection are e.g. from 8.0 to 0.8 Angstrom. For electron density studies, the latter number can be 0.5 or 0.4 Angstrom, but never lower than half of the wavelength. For badly diffracting crystals, it could be 1.0 or 1.2 Angstroms (at above 1.2A structure solution using direct methods is "impossible"). The first number is mainly dependent on the virtual size of the beam stop. For measurements at dx=25 mm with a 65mm KappaCCD with the smallest beam stop in its "closest" position, no diffraction can be seen above 7.0 Angstrom. A bigger beam stop makes this limit much lower, shifting the beam stop further away from the crystal (even by a few mm) can make this limit very much higher.

These two parameters are there to warn users when they are doing unusual things: A minimum value of the first number (minimumlowresolution) and a maximum value of the last number (maximumhighresolution).

The defaults are set fairly permissive. If you want to be warned before, you can make these values more strict.

maxusdcbug

maXus and collect both had a bug in the handling of direction cosines. These bugs compensated for 100%, such that everything worked fine. However, the direction cosines are now mis-arranged in the CIF file. By setting this variable to "0", this can be fixed on the collect side (but buggy versions of maXus will not be able to read the corrected CIF files!).

mindiskspace

Some programs will check whether there is some disk space when they start, but without knowing how much space they will need. The setting of mindiskspace is the number of bytes they will require to be free in the working directory before they will start any work.

minscanserieslength

For small molecule structures, more than a few images are needed in any scan series. Therefore series shorter than 5 images are ignored where looking for scans in the "makesav" and "nprocess" programs. For proteins or very big small molecules this can be set to 1.

nottooclose

If this parameter is set to 1, the default dx for data collection strategy is verified to cover the detector with data. If the detector is large enough, it will be moved back.

If this parameter is set to 0 (the default), all measurements are always proposed to be performed at the closest possible distance.

nprintformats

The list of graphics formats supported by nprint. If you add any, make sure they are properly supported by the ImageMagick software.

orientdegreetime

Default scan time in seconds per degree used in the orientation and single scans experiment in collect.

orientdx

default crystal to detector distance for orientation experiment (mm). The standard value is "far away" to get largest orientational freedom for the crystal to make orientation easy. If you frequently use the orientation experiment to make rotation photo's, you might want to set this value lower. If the value specified is higher than the maximum dx of the machine, it is set to dxmax-5.

orientndispcell

Selects whether the "orientations and single scans" experiment in collect should start "ndisp" with (1) or without (0) unit cell.

orientscanwidth

Default scan width (degrees) used in the orientation and single scans experiment in collect.

overloadframetime and overloadthetafraction

The button in "collect" that extends a strategy by a set of quicker scans to re-measure expected overflows is configured by these two variables. First, the data set to be quickly recollected is reduced by the "overloadthetafraction" (e.g. if you are collecting data up to 27.5 degrees in theta, the reduced data set will normally contain data up to 0.5*27.5=13.75 degrees in theta). Then the data collection time is "modified" by the setting of "overloadframetime". Overloadframetime is by default given as "('multiply',0.1)". Here, 0.1 is the multiplication factor, hence the overload frames will be collected 10 times faster than the rest of the data. Alternatively, this can be set to "('replace',5)". In this case the overload frames will be collected at 5 seconds per frame.

ownxdisp

Nprocess can use "xdisplayf" to show the progress of the integration. If "ownxdisp" is set to 1, nprocess will start and kill xdisp for you. If "ownxdisp" is set to 0, nprocess will communicate with an existing xdisplayf program.

phichiindexfit and phichilevelfit

These are the dirax parameters "indexfit" and "levelfit" as they are used by the phi/chi procedure. These might need relaxing in some cases.

phichiintcrit and phichiradcrit

These are the default values that the phichi program uses for its intcrit and radcrit criteria.

processtogether

The nprocess program asks denzo to process a number of frames as one set. The parameter "processtogether" should be set to the number of degrees of data you "normally" want to process as a unit. For small molecules 15-20 degrees is reasonable. For minerals you might want to go even larger. For proteins 1-2 degrees might be sufficient.

nreportfooter and nreportheader

The nreport program uses these strings as the start and end of the HTML reports it generates. They can be customized to localize the reports to your lab. Please note that using "triple double quotes" to delimit these strings makes it possible to use multiple lines of text

nreportheader="""like
this"""

packettimeout

The timeout in seconds for receiving a network packet from the hardware server. If your hardware server is far away, this may need to be increased. This number must be at least 10 seconds higher than the packet timeout configured in the KappaCCD server software.

peakradiusfactor

The multiplication factor to calculate the radius of the area to be integrated from the single sigma peak radius. Should not be changed from the default value of 2.2

peakrefexpert

Set this to 1 if you know all of the intrinsics of the peakref program. In that case the "npeakref" program will show a command line.

powderformat

Switches the default output format of powderize.

• standard: lines containing "2 theta", "intensity" and "number of pixels contributing to this intensity".
• xrs82: lines containing "2 theta" and integer "intensity". For compatibility with GUFI.

profilefitradius

Specifies the denzo "profile fit radius" that denzo should use. If the reflections look very different on different areas of the detector, you might want to lower this value. Otherwise the default should be fine.

psviewers

A list of postscript viewers to look for when displaying a postscript file.

readoutnoise

The readout noise that is used in the dezingering algorithm in case the header of the image does not specify a readout noise by itself. This value is given in ADU's. A reasonable value is 3.0, which is the default.

reportsquarer

If set to 1, makes nreport report the "square" r-factor from scalepack instead of the default "linear" r-factor.

resolution

default desired resolution for dataset (Angstrom). The default value corresponds to 27.5 degrees for Mo, and 90 degrees (full sphere) for Cu radiation.

resolutioncircleradius

A set of 5 numbers indicating the resolution where resolution circles should be proposed by default by the ndisp program. A value of 0 can be used to draw less than 5 resolution circles.

resomode

Some people prefer to see resolution in Angstrom, other people prefer to think in terms of the diffraction angle theta. The behaviour of the "collect" programs in presenting resolutions can be configured using the resomode variable.

• "resomode=0": If a program asks for a resolution in Angstrom, ask for a resolution in Angstrom; if a program asks for a theta angle, ask for a theta angle. This is the default setting.
• "resomode=-1": Ask for a theta angle, even when the underlying value required is a resolution.
• "resomode=1": Ask for a resolution, even when the underlying value required is a theta angle.

scalemerge

If this is set to 1, scalepack will be instructed to merge equivalent data unless "direction cosines" are requested. If this is set to 0, scalepack will never merge data. Please note that for merging, scalepack will automatically down-weight outliers, and this procedure will generally result in slightly better data than plain merging the data would do.

scalerestrain

The default restraint value to be used by "scalepack" for inter-frame scaling. This should be set to the "expected difference in the scale between successive frames". On a KappaCCD this should most probably be very tight, except if you are using scalepack to perform absorption correction.

scanrepr

Scans can be represented as a pair (beginposition,endposition), or as (beginposition,scanlength). The parameter "scanrepr" can be set to 0 for the former, and 1 for the latter representation. Setting it to 2 will give a combination of both: (begin, length, end) [Nice, but takes a lot of space on the screen].

scanrmat

The default setting (1=enable, 0=disable) of the scanrmat option of the makeshoe program.

scanwidthtolerance

Before collecting an image, "collect" will check whether an image that is already present on disk with the same name is identical. An angle-tolerance is used to decide whether the scan to perform for a frame to be measured is identical to the scan found in the header of an already collected image. The "scanwidthtolerance" is expressed as a fraction of the total frame angle.

showtotalrefls

If set to 1, "collect" will always show the total number of reflections it is dealing with, and not the "reduced" number that it is using for strategy calculations.

spotradius

spot radius used in denzo runs from the GUI. If the value is 0 (the default), then a reasonable spot radius is calculated from the spot size in the frames that are studied (peak search, findresolution).

viewposition

The default view position used by "collect". The positions of the phi, theta, omega and kappa motors can be specified in degrees, and dx in mm. If the specified value for dx is negative, it will be counted from the back of the dx-sled.

weaklevel

Defines the default "weak level" used in denzo and for the postrefine program. This determines the minimum intensity (in terms of I/sigma) of spots before they are used in cell refinement and profile fitting.

webbrowsers

Sets a list of webbrowsers to try for the help functions in the GUI programs. This can only be "mozilla" or "netscape" because the collect suite will try to use complex command line arguments that only these two browsers know.

acceptdenzosign=0
anglemargin=1.5
anyexpert=0
autoconnect=1
autodark=0
autostartserver=1
axcrit=0.2
backgroundradius=0
cellaskkcdfilename=0
cellrefinedetector=0
chiralonly=0
cifinoutput='import.cif'
ciftype='maxus'
completeness=0.995
defaultdatacollectionstrategy=0
defaultwavelength=0.71073
denzoindexcesd=1
detectorsizemargin=1.5
dxfactor=1.2
dxlimit=300
exposuretimetable=[20,60,120,600]
gamma=1.4
generatorcheckdx=35
generatorcheckpixels=50
generatorcheckzingers=1
gonzeroaction=9
iboxsize=24
imageextension='.kcd'
inhibitgc=1
kcddatatype=None
licensewarning=90
localcifdata=''
mailrecipient='ccd'
maximumhighresolution=2.0
maxusdcbug=1
mindiskspace=1000000
minimumlowresolution=4.0
minscanserieslength=5
momaxaxis=10.0
nottooclose=0
nprintformats=['ps','ppm','png','jpg']
nreportfooter="""<HR><ADDRESS>...</ADDRESS></BODY></HTML>"""
nreportheader="""<HTML><HEAD><TITLE>One page report</TITLE></HEAD><BODY>"""
orientdegreetime=5
orientdx=999
orientndispcell=1
orientscanwidth=2
overloadframetime=('multiply',0.1)
overloadthetafraction=0.5
ownxdisp=1
packettimeout=30
peakradiusfactor=2.2
peakrefexpert=0
phichiindexfit=2
phichiintcrit=0.5
phichilevelfit=1000
phichiradcrit=0.16
powderformat='default'
processtogether=15
profilefitradius=16.0
psviewers=["kghostview","gv","ghostview"]
readoutnoise=1.0
redundancy=1.
reportsquarer=0
resolution=0.77
resolutioncircleradius=(7.0,1.2,0.77,0,0)
resomode=0
scalemerge=1
scalerestrain=0.002
scanrepr=1
scanrmat=0
scanwidthtolerance=0.003
showtotalrefls=0
spotradius=0
viewposition={'phi':-74.66,'theta':0,'omega':105.340,'kappa':-46.224,'dx':-5}
weaklevel=10
webbrowsers=["mozilla","netscape"]

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