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DIP2000 user manual |
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Log in on the computer which is attached to the DIP2000 system. Check that enough disk space is available for your work with the command % df. For a DIP2020 each (uncompressed) image takes up 12.5 Mb, so for 180 images of 1, one needs 2.25Gb disk space. For a DIP1030 or DIP2030 each (uncompressed) image takes up 18.0 Mb, so for 180 images of 1, one needs 3.24Gb disk space.
Set the default directory on a disk with sufficient space. The disk on which the images should be written should not be nfs mounted, since the reading of the image could be hampered by a too slow network. The image data disk should therefore be directly connected to the computer which is used for data collection.
To set up an appropriate subdirectory to work in (e.g. the project one works on) and to copy some files relevant for data collection and processing one can now run a command file, which copies these files into a directory which is made for your project. This can be done by typing :
% dipprep
This command file will prompt for a project name, make a directory of that name and set you in a subdirectory called "images". At the same time it will copy some denzo command files in the "project" directory. dipprep is an alias for % source ~/DIPprep. An example of a file DIPprep can be found in the Appendix. This script will have put you in the directory where you will do the collection of images.
Start the DIP2000 program by typing "xpress" at the prompt e.g.:
/disk2/xdip/prot/images> xpress
The program starts with the GUI front end of the data collection software.
It will display a bar with control buttons at the top of the screen.
The left, green part is for the operation of the generator. This part has not yet been implemented. It should not be closed however, since this part also takes care of the error messages of the program.
The middle, blue part is for the two devices attached to the generator, device A and device B. The DIP2000 is controlled as device A. Operation of the DIP2000 will therefore be done by pulling down the menu from the button marked Device A.
Off-line operations like e.g. display and analysis of images can be done from the button marked with the pencil.
The red right button is an emergency button for the generator. If this button is pressed all actions of the goniostat and scanner will be stopped immediately..
In the winterm window from which xpress has been started a list
of commands and replies will pass which echo the communication between
the controller and the computer. This window will be referred to as the
"LINEEYE" window. This is useful to see whether something is happening
and in some cases for trouble shooting, because one can see which command
has been executed as the last one. An explanation of these commands can
be found in Appendix 1.
The data collection program on the DIP2000 is written with the OpenWindows window manager. This program has the following conventions :
Two kind of buttons can be distinguished : Rectangular boxes and (triangular) arrows. The boxes allow for one choice only and should be clicked with the left hand mouse button. The arrows are pointing to pull down menus with several choices and these should be pulled down with the right hand mouse button. Pushing the left hand mouse button on an arrow means that one selects the top choice of the pull down menu, which is not always what one wants.
An example : If one would push the right hand mouse button on
the Device A button, two possibilities appear : Initialize/Manual
and Standard Datacollection. The first one will pop up three windows
(see below), the second one will pop up one window. If one would use the
left
mouse button, the first choice would be taken automatically and the three
windows will appear on the screen.
Put a crystal on a goniometer head. The crystal must be mounted on a goniometer head which, in the case of a kappa goniostat, is capable of being translated along the Phi axis, and for all goniostats, in two mutually perpendicular directions normal to that axis. Put the goniometer head on the goniometer and screw it on. Put the crystal on the same height as the tip of the collimator. The crystal should be centred optically with the microscope or the CCD camera.
Put the mouse on the box Device A and press the right mouse button.
Select Initialize/Manual. This pops up three screens : The Setup window,
the Instrument status screen and the Manual Control window, which are shown
below.
If the axes read-out in the DIP2000 system status list is blank (as shown above), the axes have lost their zero position and cannot be read out properly. This can be the case if the interface has been switched off. The axes can be set to zero by pressing the Setup start button in the DIP2000 setup window.
The windows should then look like as follows:
To centre the crystal, the crystal shoudl be viewed at 0 and 180 degrees and at 90 and 270 degrees. The phi axis can be moved by hand in the case of a phi axis goniostat. here one can uncouple the goniometerhead by releasing the allen screw between the two screws just at the base of the goniometer head. Use the smallest allen key from the set to unscrew it. Put the phi axis at the angle where the screw is best accessible before doing this (180 deg. for older systems, 0 deg. for later models). Once unscrewed, the phi axis can be rotated manually to posistions 180 deg. apart. Do not forget to fix the phi axis again after centering, because the Phi axis controlled from the computer is more reliable with a fixed Phi axis.
To move the phi axis under computer control, one needs the Basic
Operations window. Put the mouse in the Manual control box and left
click the button Basic Operation. This will pop up the following
window:
In this window you can go to Phi axis operation--> Setting angle (deg), fill in the desired value for Phi and press the Start button.
With Kappa goniostat systems you can use the manual control box which allows for fast or slow movement of each of the three goniostat axes.
Setting up for data collection
Click on the Quit button to get out of the Basic Operations screen.
Right-click the button of Device A, and drag the cursor to Standard Measurement, followed by "DIP Measurement. The following window will appear on the screen.
If a file DIP.DCL is present in the working directory, which should be the case after running the command file dipprep, the parameters stored in this file will be displayed in the data collection window. If no file DIP.DCL is present, and hence no measurement parameters are known, the file list and display of the parameter input space will be empty. In this case, LEFT-CLICK the Insert button.
Select the rotation image by a Left-click of the filename in the file list. This will popup the setup window of the rotation image. In this window one can fill in or edit the following parameters by a Left-click on the box Edit.. Edit the parameters and press the Apply button to save the modified parameters.
Editing measurement parameters
When Edit is selected from the Measure/Edit box in the upper left part of the screen, input can be done into the parameter input spaces on the lower part of the screen. Select the parameter to be edited from the list, then edit it. When parameters have been changed, press the Apply button, to store the changed values.
Each measurement parameter from the above shown window is pointed out
below.
(a) Photo
LEFT-CLICK to select the type of image to be taken as "Still" or "Rotation".
(b) IP file name
The file name to be used to write the image file on disk. Here you could
use a name like "crystalname_nnn.ipf". The 3 characters before the dot
(in this case nnn) will be changed to serial numbers starting from 001.
An example is shown below.
IP Filename : rotnnn.ipf
Starting frame number : 1
Finishing frame number : 5
Images written to disk :
rot001.ipf, rot002.ipf, rot003.ipf, rot004.ipf, rot005.ipf
Beware : When multiple images are taken sequentially as in the example above the next exposure will overwrite already present files, unless the initial number of the file is incremented by changing the parameter under Starting frame number.
When the file name starts with "@" or ends with ".", output will be used as such without conversion to serial numbers. In this case also care must be taken because the file will be overwritten by the next exposure if the file name is not changed. This maybe useful for testing purposes, if one wants to make many exposures without filling up the disk.
Note that when making stills, there is no Starting and finishing frame
number, so this always starts with 1. If you would like to make a series
of exposures, it is easier to change a character previous to one of the
last three characters to prevent previous images from being overwritten.
(c) Comment
This comment line will be put in the tail record of the image data.
Useful for generator settings, temperature etc. It can be viewed by pressing
the Info button in the Display program.
(d) Wavelength (Å)
Here one should input the X-ray wavelength used in the measurement in
Ångström. For Copper this should 1.54178, for Molybdenum this
value is 0.71069. This value is treated as a comment and has no influence
on the data collection.
(e) Distance (mm)
Here you should give the crystal to detector distance of the measurement.
Note that there is no feedback on the distance, so make sure the distance
you fill in is correct. For kappa systems a double-check is made on the
distance which is filled in in the Basic Operations window. To be entirely
sure the right distance is filled in, first enter the value in the Basic
Operations window.
(f) Monochromator
Here one should input the type of monochromator, e.g. Graphite or Mirror-mirror.
This line is treated as a comment.
(g) Diam. of collimator(mm)
Here one should input the diameter of the collimator used in the measurement. Usually a 0.3 or 0.5 collimator is used. This is treated as a comment.
The parameters (c) through (g) are attached to the image data at the time of execution and so are recorded in the tail of the IP file. These items have no influence on the control of the instrument.
The following items do influence control of the instrument for measurement.
(h) Phi/Omega start angle (deg)
Here one should input the phi (or omega) angle for the first frame.
This is the starting angle for phi (or omega) for oscillation for frame
#1. If the value after "Starting Frame Number" is not equal to zero, then
the starting value of the oscillation will be :
Phistart + {(Starting Frame Number - 1) (Rotation Range)}.
Some examples :
Phi start = 0, rotation range = 1, interval = 1, starting frame number
= 1 : This will result in the data collection starting at Phi=0.
Phi start = 5, rotation range = 1, interval = 1, starting frame number
= 1 : This will result in the data collection starting at Phi=5.
Phi start = 0, rotation range = 1, interval = 1, starting frame number
= 6 : This will result in the data collection starting at Phi=5.
Phi start = 5, rotation range = 1, interval = 1, starting frame number
= 6 : This will result in the data collection starting at Phi=11.
(i) Rotation range
Here one should input the oscillation range of phi. Normally in the
range of 1 degree for proteins, and in the range of 2 - 6 degrees for small
molecules.
(j) Interval (deg)
This is the interval between successive oscillation images. For a consecutive rotation this should be equal to the rotation range. If not, then Phistart(n) = Phistart(n-1) + Interval. An example :
Phi(start) = 0, Rotation range = 6, Interval = 12, starting frame number
= 1, Finishing frame number = 4, would make the following oscillations
:
Image 1 : 0 - 6
Image 2 : 12 - 18
Image 3 : 24 - 30
Image 4 : 36 - 42
It is also possible (but generally not necessary) to have overlap in the images, e.g. Phi(start) = 0, Rotation range = 1.5, Interval = 1, starting frame number = 1, finishing frame number = 4, would make the following oscillations :
Image 1 : 0 - 1.5
Image 2 : 1 - 2.5
Image 3 : 2 - 3.5
Image 4 : 3 - 4.5
(k) Speed (deg/min)
Here one should input the oscillation speed for Phi. This determines
the exposure time for each frame. It should not be lower then 0.004.The
exposure time is updated as a function of the speed.
(l) Repetitions
Here one should input the number of Phi oscillations. The number counts
oscillation in one direction as 1. Therefore a complete cycle is counted
as 2. The exposure time is updated as a function of the speed. Usually
one can take a value like 1 or 3.
(m) Exposure time (sec)
For rotation images, the exposure time will be calculated from the values
in items (i), (k) and (l) and it will be displayed on the line after exposure
time. For a given rotation/oscillation range one should therefore change
the exposure time by playing with the parameters Speed and Repetitions.
The exposure time when taking a still photo can be filled in straight away.
(n) IP position (deg)
This designates the IP offset position when a still or rotation image
is taken. For instruments supporting the IP-offset, the value should be
between 0 and 20 degrees (some systems -20 to 0) or -30 to 30 for Weissenberg-type
systems.
(p) Total number of frames (Still only)
The total number of frames to be measured when taking still images.
(q) Starting frame number
When measurement is to start from the beginning, fill in 1. To start
from frame number "n" input the value of n. See also Phi start for the
relation between Phi start and Starting Frame Number. If for any reason
a data collection has stopped after n frames, one can easily change Starting
Frame Number to n+1 to continue the data collection from the point where
it was stopped.
(r) Finishing frame number
This designates the final frame number of the measurement. For a collection
of 90 images, numbered 1 to 90 one would input 90 here.
If all the parameters have been filled in, one can press the Apply" button. This will save all the revised parameters.
Make sure the Main shutter of the generator is open. Then press Measure.
This will start the collection of images. Pressing the History button will
give information on the data collection process. There are three levels
of amount of information. The exposure time button displays the time remaining
for the current exposure.
If for some reason one would not be happy with the data collection parameters and data collection is busy, one can stop the measurement by clicking the Stop button. This will "grey" the Stop button. The data collection will continue until the current process (e.g. erase, positioning or read-out) is finished, and then control will be given back to the user. It may therefore take a while before the process actually stops. If it is finished, the Stop button is clear again and you should be able to collect new images.
Pressing Ctrl-C in the xpress window is not recommended. If you do, the DIP2000 may hang up, because not all the processes have been properly closed and the deamon of the image transfer, dip2000_srv, may still be hanging around. To overcome this you can run the program dipclean which checks for these processes and kills them.
Note :
The DIP2020 and DIP2030 have a built in 2 offset capability, which is particularly useful for collecting high resolution data. This offset is input as IP position in the data collection menu. The maximum allowable values are 30 for older systems and 0-20 for newer systems. This corresponds to a 7 cm (DIP2020) or 10 cm (DIP2030) vertical displacement of the image plate Systems with the window extended upwards should use IP position between 0 and 20. For systems with the window extended downwards the IP position should be between 0 and -20.
To process images with DENZO, two lines of parameters should be changed :
x beam and y beam
detector rotz.
The x-beam and y-beam values change as a function of the IP position. In Appendix 5 the primary beam position is listed as a function of the pseudo 2 offset.
The value of detector rotz should be opposite to the value of IP offset (e.g. 15, when IP-offset is -15).