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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8"><title>iMosflm Tutorial</title>
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<div style="text-align: center;"><big><big><big><font face="Times New Roman, serif">iMosflm
Tutorial<br>
<small>for version 7.4.0 January 2021</small><br>
</font></big></big></big>
</div>
<br>
<big><big>Table of Contents</big></big><br>
<ul id="mozToc">
<!--mozToc h1 1 h2 2 h3 3 h4 4 h5 5 h6 6-->
<li><a href="#mozTocId29715">1.
Introduction</a>
<ul>
<li><a href="#mozTocId534381">1.1
Background</a></li>
<li><a href="#mozTocId827268">1.2
Installation</a></li>
<li><a href="#mozTocId410751">1.3
Documentation</a></li>
<li><a href="#mozTocId816121">1.4
Aims of the tutorial</a></li>
<li><a href="#mozTocId689712">1.5 Mouse and key
functions </a></li>
</ul>
</li>
<li><a href="#mozTocId360577">2. Overview
of iMosflm</a>
<ul>
<li><a href="#mozTocId626255">2.1
Drop Down menus</a></li>
</ul>
</li>
<li><a href="#mozTocId486119">3. Adding
images to a session</a>
<ul>
<li><a href="#mozTocId215473">3.1 Summing images
when reading hdf5 files (chunking) </a></li>
</ul>
</li>
<li><a href="#mozTocId44996">4. Image
Display</a>
<ul>
<li><a href="#mozTocId114918">4.1
Display Icons</a>
<ul>
<li><a href="#mozTocId74027">4.1.1
Masked areas - circular backstop shadow</a></li>
<li><a href="#mozTocId23713">4.1.2
Masked areas - general exclusions</a></li>
<li><a href="#mozTocId209370">4.1.3 Spot
search area</a></li>
<li><a href="#mozTocId890852">4.1.4
Resolution limits</a></li>
<li><a href="#mozTocId746242">4.1.5 Zooming
and Panning</a></li>
<li><a href="#mozTocId310974">4.1.6
Circle fitting</a></li>
<li><a href="#mozTocId822853">4.1.7 Phi
profile</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#mozTocId150573">5. Spot
finding, indexing and mosaicity estimation</a>
<ul>
<li><a href="#mozTocId591049">5.1
Spot Finding</a>
<ul>
<li><a href="#mozTocId495561">5.1.1
If the spot finding has not worked well </a></li>
</ul>
</li>
<li><a href="#mozTocId325663">5.2
Indexing</a>
<ul>
<li><a href="#mozTocId798805">5.2.1
If the indexing fails - Direct beam search</a></li>
<li><a href="#mozTocId960714">5.2.2
If the indexing fails - Other parameters.</a></li>
</ul>
</li>
<li><a href="#mozTocId189423">5.3 Indexing
multiple lattices simultaneously</a>
<ul>
<li><a href="#mozTocId774580">5.3.1
Practical Tips</a></li>
</ul>
</li>
<li><a href="#mozTocId863376">5.4 Known
cell option</a></li>
<li><a href="#mozTocId368904">5.5
Space group selection</a></li>
<li><a href="#mozTocId878705">5.6
Mosaicity estimation</a>
<ul>
<li><a href="#mozTocId5079">5.6.1
The mosaic block size</a></li>
<li><a href="#mozTocId431248">5.6.2 The phi profile</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#mozTocId958696">6. Saving and
recovering a session</a></li>
<li><a href="#mozTocId38147">7. Data
collection strategy</a>
<ul>
<li><a href="#mozTocId646178">7.1
Evaluating completeness manually</a></li>
<li><a href="#mozTocId581133">7.2
Calculating a strategy automatically</a></li>
<li><a href="#mozTocId750492">7.3
Calculating a strategy using multiple crystals</a>
<ul>
<li><a href="#mozTocId126775">7.3.1 Calculating a
strategy when some data have already been collected and processed</a></li>
</ul>
</li>
<li><a href="#mozTocId992584">7.4
Calculating a suitable oscillation angle</a></li>
</ul>
</li>
<li><a href="#mozTocId610524">8. Cell
refinement</a>
<ul>
<li><a href="#mozTocId853572">8.1
Selecting the images</a>
<ul>
<li><a href="#mozTocId721787">8.1.1
Manual selection</a></li>
<li><a href="#mozTocId716779">8.1.2
Automatic selection</a></li>
<li><a href="#mozTocId766179">8.1.3
Graphical selection (Not recommended)</a></li>
</ul>
</li>
<li><a href="#mozTocId639269">8.2
Integrating the images and refining the cell</a>
<ul>
<li><a href="#mozTocId109529">8.2.1
The detector parameters window</a></li>
<li><a href="#mozTocId251279">8.2.2
The crystal parameters window</a></li>
<li><a href="#mozTocId957382">8.2.3
The central spot profile</a></li>
<li><a href="#mozTocId943675">8.2.4
The summary window</a></li>
<li><a href="#mozTocId657403">8.2.5
The final results</a></li>
</ul>
</li>
<li><a href="#mozTocId325680">8.3 Refining cell parameters for
multiple
lattices</a></li>
<li><a href="#mozTocId775517">8.4 If the
prediction for the first image of a segment is poor</a></li>
</ul>
</li>
<li><a href="#mozTocId907047">9. Integration</a>
<ul>
<li><a href="#mozTocId261793">9.1
Image selection</a></li>
<li><a href="#mozTocId647795">9.2
Setting the MTZ filename and controlling updating of the image
display</a></li>
<li><a href="#mozTocId164196">9.3
Integrating the images</a></li>
<li><a href="#mozTocId820258">9.4
Parameter display windows</a></li>
<li><a href="#mozTocId595790">9.5 Integrating the whole dataset</a>
<ul>
<li><a href="#mozTocId15993">9.5.1 Parallel Integration Using
multiple cores</a></li>
<li><a href="#mozTocId245100">9.5.2
Integrating as a background job</a></li>
</ul>
</li>
<li><a href="#mozTocId905962">9.6
Checking the integration</a></li>
<li><a href="#mozTocId324820">9.7
Advanced features for integration</a></li>
<li><a href="#mozTocId906112">9.8
Integrating multiple lattices</a></li>
</ul>
</li>
<li><a href="#mozTocId868502">10. Running
Pointless to check the symmetry</a></li>
<li><a href="#mozTocId420086">11. Running
Aimless to scale and merge the data</a></li>
<li><a href="#mozTocId49119">12. History
and mosflm log file</a></li>
<li><a href="#mozTocId112431">13. Warning
Messages</a></li>
<li><a href="#mozTocId251449">14. Useful command line options</a>
<ul>
<li><a href="#mozTocId323598">14.1 The site file</a></li>
</ul>
</li>
<li><a href="#mozTocId979076">15. The mosflm SUMMARY file</a></li>
<li><a href="#mozTocId464596">16. Scaling
data with CCP4i</a>
<ul>
<li><a href="#mozTocId16713">16.1
Looking at the AIMLESS output</a></li>
</ul>
</li>
<li><a href="#mozTocId44933">17. Changing
the symmetry</a></li>
<li><a href="#mozTocId252763">18. Looking
at the CTRUNCATE output</a></li>
<li><a href="#mozTocId991006">19. If you
have time ...</a>
<ul>
<li><a href="#mozTocId52124">19.1
Different mosaic spreads</a></li>
<li><a href="#mozTocId530274">19.2
Checking up on outliers</a></li>
<li><a href="#mozTocId364567">19.3
How accurate does the unit cell have to be?</a></li>
</ul>
</li>
<li><a href="#mozTocId727216">20. Tips</a></li>
<li><a href="#mozTocId654806">21. Known Bugs</a></li>
<li><a href="#mozTocId11307">22. Processing Electron Diffraction
images</a></li>
<li><a href="#mozTocId154054">Appendix I</a></li>
</ul>
<br>
<h1><a class="mozTocH1" name="mozTocId29715"></a><font face="Times New Roman, serif">1.
Introduction</font></h1>
<h2><a class="mozTocH2" name="mozTocId534381"></a><font face="Times New Roman, serif"><font size="4"><b>1.1
Background</b></font></font></h2>
<p>MOSFLM can process diffraction images from a wide range of
detectors and produces, as output, an MTZ file of reflection indices
with their intensities and standard deviations (and other
parameters). This MTZ file is passed onto other programs of the CCP4
program suite (POINTLESS, AIMLESS, CTRUNCATE) for further data
reduction.</p>
<p>The MOSFLM program was originally written to process data
collected on film, largely by Alan Wonacott. It was then modified
to
process data collected
using the image plate detector developed at the EMBL outstation in
Hamburg by Jules Hendrix and Arno Lentfer. This is the current version of the program, which will
also process data from CCD and hybrid pixel detectors.</p>
<h2><a class="mozTocH2" name="mozTocId827268"></a><font face="Times New Roman, serif"><font size="4"><b>1.2
Installation</b></font></font></h2>
<p>The new GUI (iMosflm) is currently available for Windows, Mac OSX
and Linux platforms. For details of installation visit
<a href="http://www.mrc-lmb.cam.ac.uk/mosflm/imosflm">http://www.mrc-lmb.cam.ac.uk/mosflm/imosflm</a><br>
</p>
<h2><a class="mozTocH2" name="mozTocId410751"></a><font face="Times New Roman, serif"><font size="4"><b>1.3
Documentation</b></font></font></h2>
<p>There are two distinct sources of documentation for MOSFLM,
although neither of these currently makes any reference to the new
GUI. At present, this document is the only documentation available
for iMosflm. <br>
</p>
<p><span style="font-weight: bold;">Also, only this document is updated
for new features of MOSFLM since version 7.0.9 (June 2012).</span> </p>
<ol>
<li>
<p>The MOSFLM user guide. This is available as a plain text
file (mosflm_user_guide.txt) or on the web
(<a href="http://www.mrc-lmb.cam.ac.uk/mosflm/mosflm">http://www.mrc-lmb.cam.ac.uk/mosflm/mosflm</a>/)
as a PDF or HTML document. This
contains considerably more detail about how ipmosflm processes
diffraction images than this tutorial does. It is a very good idea to
look through this guide before starting serious data processing with
MOSFLM, although you do not need it for this tutorial. This has not
been updated since version 7.0.9 (June 2012).<br>
</p>
</li>
<li>
<p>The "on-line" help. If you type "help" at the "MOSFLM =>"
prompt (after starting the program mosflm) all possible keywords are
listed, with information on each keyword. This information is stored in
an ASCII file (mosflm.hlp) which can also be read (and searched) with
an editor. This relies on having the environment variable
"CCP4_HELPDIR" set to the directory containing this file. This is also
available on the MOSFLM web pages under "keyword synopses"</p>
</li>
</ol>
See
also: <br>
Powell, H.R., Battye, T.G.G., Kontogiannis, L., Johnson, O. &
Leslie, A.G.W. 2017 Integrating macromolecular X-ray diffraction data
with the graphical user interface iMosflm. Nature protocols 12,
1310-1325. <br>
This has examples of processing "difficult" datasets that can be
downloaded from the website.<br>
<br>
Battye, T.G.G., Kontogiannis, L., Johnson, O., Powell, H.R. &
Leslie, A.G.W. 2011. iMosflm: a new graphical interface for diffraction
image processing with MOSFLM. Acta Cryst. <span style="font-weight: bold;">D67</span>, 271-281.<br>
<h2><a class="mozTocH2" name="mozTocId816121"></a><font face="Times New Roman, serif"><font size="4"><b>1.4
Aims of the tutorial</b></font></font></h2>
<p>Your task is to process 84 images, hg_001.mar1600 to
hg_084.mar1600, collected on a Mar345 image plate detector at a
synchrotron beamline. These are crystals of a small domain (91 amino
acids) that have been soaked in a mercury compound, resulting in a
dataset with a strong anomalous signal which can easily be used to
solve the structure. These images have kindly been provided by
Camillo Rosano. <br>
</p>
<p>Note: You can equally well choose to process your own diffraction
images if you wish </p>
<h2><a class="mozTocH2" name="mozTocId689712"></a><font face="Times New Roman, serif"><font size="4"><b>1.5 Mouse and key
functions<br>
</b></font></font></h2>
For simplicity, the mouse and key functions are
all described here, although they will also be referred to at various
points in the tutorial.<br>
<br>
When positioned over the image, right mouse button will return the
display to the full size image if it has been zoomed. Scrolling middle
mouse will zoom/shrink the image.<br>
Holding down the "Ctrl" key (or "Alt" or "Cmd" (for Macs)) will display
the resolution and the current mouse position on the image
in mm and pixels. If positioned over a found spot (at the indexing stage), the spot coordinates
and I/σ(I) will be given. If positioned over a predicted spot position
(after indexing) the <i>hkl</i> indices will be shown.<br>
Holding down the "Shift" key while the "Zoom" icon in the image is
selected will show the image within
the small dotted square zoomed within the solid square.
<br>
<br>
<h1><a class="mozTocH1" name="mozTocId360577"></a><font face="Times New Roman, serif">2. Overview
of iMosflm</font></h1>
<p>Start the program by typing "imosflm". After a brief
pause, the following window will appear (note, the date and version
will be different):</p>
<p><img src="images/img_001_2.0_overview.png" name="graphics1" solid="" align="left" border="0" width="100%">The
basic operations listed down the left hand side (Images, Indexing,
Strategy, Cell Refinement, Integration, History) can be selected by
clicking on the appropriate icon, but those that are not appropriate
will be greyed-out and cannot be selected.</p>
<h2><a class="mozTocH2" name="mozTocId626255"></a><font face="Times New Roman, serif"><font size="4"><b>2.1
Drop Down menus</b></font></font></h2>
<p>Clicking on "Session" will result in a drop-down menu
that allows you to save the current session or reload a previously
saved session (or read/save a <a href="#mozTocId323598" target="_blank">site file</a><a href="#mozTocId323598" target="_blank">
</a>(see §14.1) or add images, or since 7.2.0, write a spots file):</p>
<p><img src="images/img_002_2.1_session.png" name="graphics2" align="bottom" border="0" height="324" width="534">
</p>
<p>Clicking on "Settings" will allow you to see (and
modify) Experiment settings, Processing options and Environment
variables. <br>
</p>
<p><img src="images/img_003_2.1_settings.png" name="graphics54" align="bottom" border="0" height="106" width="190">
</p>
<p>The "Experiment settings" option has two tabs, Experiment and
Detector. <br>
</p>
<p>In the Experiment tab, experimental parameters (beam position,
detector distance, beam divergence and polarisation, wavelength and
detector Two Theta angle can be modified. There is also a tick box to
deal with beamlines where the phi rotation is in the opposite sense to
the conventional one. These parameters are read from the image header,
but if they are wrong they can be corrected here.</p>
<p>The Detector tab lists the current values of the refineable detector
parameters, the detector gain, ADC offset and pixel size (in mm). There
is a "Reset" button that will reset all refineable detector parameters
to their initial values. This should be used if parameters have refined
to unreasonable values, either because they are poorly defined or
because an incorrect indexing soltuion has been used to integrate
images. A pop-up warning message will be given in such cases, and
parameters can also be reset from this pop-up window.</p>
<p>Note: If information in the image headers is incorrect, some of the
parameters can be read from a "<a href="#mozTocId323598">site file</a>"
so that they do not have to be entered manually for every iMosflm
session. If the phi
values are not correct (e.g. all values are zero) the correct values
can be set by editing the phi values for the first image (see Advanced
Usage box in the following section).<br>
</p>
<br>
<p><img style="width: 475px; height: 570px;" alt="" src="images/img_003b_2.1_reset.png"><br>
</p>
"Processing options" will open a window with six tabs: Spot finding,
Indexing, Processing, Advanced refinement, Advanced integration and
Sort Scale and Merge. This allows parameters associated with these
processing steps to be changed, and provides additional options such as
pattern matching orientation refinement (see <a href="#mozTocId775517">8.4</a>),
addition of Pilatus or Eiger images to assist in spot finding or
detector parameter refinement and smoothing of missetting
angles (see <a href="#mozTocId905962">9.6</a>). Situations in which it
may be useful to modify these parameters
will be described in the appropriate section of the tutorial. A summary
is provided in the "<a href="#mozTocId727216">Tips</a>" section.<br>
<br>
<img style="width: 676px; height: 136px;" alt="" src="images/img_003c_2.1_processing_options.png"><br>
<br>
"Environment variables"will not normally require any changes.<br>
<br>
<p>The three small icons below "Session" allow you to start
a new session, open a saved session or save the current session.
Moving the mouse over these icons will result in display of a tooltip
describing the action taken if the icon is clicked.</p>
<h1><a class="mozTocH1" name="mozTocId486119"></a><font face="Times New Roman, serif"><b>3. Adding
images to a session</b></font></h1>
<p>To add images to a session, use the "Add images..."
icon: </p>
<p><img src="images/img_004_3.0_addimage.png" name="graphics3" align="bottom" border="0" height="102" width="202">
</p>
<p>Select the correct directory from the pop-up Add Images window
(the default is the directory in which iMosflm was launched). All
files with an appropriate extension (which can be selected from the
"File type") will be
displayed. <br>
</p>
<p>Note that for images where the image number is given as the
extension (eg my_xtal.001) you will need to select "Numbered files" as
the File type.</p>
<p>For Eiger HDF5 files, select the "master" file (this will normally
be the only file listed). Nexus files (written at Diamond Light Source)
are not currently handled.<br>
</p>
<p>Double-clicking on any file will result in all images with
the same template (or all images in HDF5 files) being added to the
session. The template is the
whole part of the filename prefix, except the number field which
specifies the image number. An alternative is to single-click on one
image filename and then click on Open.</p>
<p><img src="images/img_005_3.0_imgfiles.png" name="graphics4" align="bottom" border="0" height="404" width="452">
</p>
<p>To open one or several images only, check the 'Selected images
only' box and then use click followed by Shift+click to select a
range of images or Control+click to select individual image files as
required. This is not an option with HDF5 files.<br>
</p>
<p>Loaded images will be displayed in the Images window with the
start & end phi values displayed (as read from the image header) as shown below.</p>
<p><img style="width: 1082px; height: 857px;" alt="" src="images/img_006_3.0_overview.png"><br>
</p>
<p>All images with the same template belong to the same "Sector"
of data. </p>
<p>Multiple sectors can be read into the same session. Each sector
can have a different crystal orientation. </p>
<p>For the Mar images in the tutorial dataset, note that a "Warning"
has appeared. Click anywhere on
the “warnings 1” text to get a brief description of the warning.
In this case it is because the direct beam coordinates stored in the
MAR image plate images are not 'trusted' by MOSFLM and the direct
beam coordinates have been set to the physical centre of the image.
Click on the "X" on the right hand side to dismiss this
warning; click anywhere outside the warning box to collapse the box;
double-click the warning text itself to obtain more detailed information and advice on how to improve the processing.<br>
</p>
<p><img src="images/img_007_3.0_warning.png" name="graphics6" align="bottom" border="0" height="86" width="420">
</p>
<p>The direct beam coordinates (read from the image header or set by
MOSFLM) and crystal to detector distance are displayed. These values
can be edited if they are not correct.</p>
<p><img src="images/img_008_3.0_directbeam.png" name="graphics7" align="bottom" border="0" height="78" width="330">
</p>
<p><br>
<br>
</p>
<table border="2" bordercolor="#ff0000" cellpadding="2" cellspacing="2">
<tbody>
<tr>
<td>
<p><b>Advanced Usage</b> </p>
<ol>
<li>
<p>The phi values of images can be edited in the Image
window. First click on the "Image 1" line to highlight it then
click with the mouse over the phi values to make them editable allowing
new values to be given. These new values are propagated for all
following images in the same sector, assuming a constant rotation angle
per image. Starting values for the three missetting angles (PHIX, PHIY,
PHIZ) may also be entered following the image phi values.</p>
</li>
<li>
<p>To delete a sector click on the sector name to select it
(it turns blue) then use the right mouse button on the sector to bring
up a "delete" button. Move the mouse over the delete button (it turns
blue) and click to delete the sector and its images. Individual images
can be deleted from the Images pane in the same way.</p>
</li>
<li>
<p>If
one sector is added and used for indexing, and then a second sector
from the same crystal is added, the matrix for the second sector will
not be defined. To define it, double-click on the matrix name for the
first sector, save it to a file, double-click on the matrix name
(Unknown) for the new sector and read the matrix file written for the
first sector. Alternatively, it is possible to "drag and drop" the
matrix from the first sector onto the second sector (drop onto the
sector itself, not the Matrix for the second sector).<br>
</p>
</li>
</ol>
</td>
</tr>
</tbody>
</table>
<h2><a class="mozTocH2" name="mozTocId215473"></a>3.1 Summing images
when reading hdf5 files (chunking)<br>
</h2>
When reading images in hdf5 format, there is an option to automatically
sum the images prior to processing. If the oscillation angle per image
is less than 0.2°, a pop-up window as shown below will appear
suggesting that processing may work best if images are summed, and
giving various options. The number of images to be summed can also be
specified in the Settings -> Processing options -> Processing
tab. Note that the image numbers in the iMosflm plots will then refer
to "virtual" images after summation, not the original image numbers.
Generally processing will work well with an oscillation angle of 0.1°
or greater, but this allows an option to work with summed images
instead. This will speed up the processing of the dataset. <br>
<br>
This option is only available for hdf5 files, but Pilatus cbf or Eiger
(cbf or hdf5) images can be summed for the purpose of spot finding (see
I<a href="#mozTocId495561">f the spot finding has not worked well) </a>or
determining the centroid of reflections for refinement (<big><small>see
§<a href="tutorial_7.3.0.html#mozTocId109529">8.2.1</a></small></big>)
but still integrated individually.<br>
<br>
<img style="width: 562px; height: 336px;" alt="Chunking dialogue" src="images/img_008b_3.1_chunkimages.png"><br>
<br>
<h1><a class="mozTocH1" name="mozTocId44996"></a><font face="Times New Roman, serif">4. Image
Display</font></h1>
<p>When images are added to a session, the image that was selected at
the "Add images" step is displayed in a separate display window.</p>
<p><img src="images/img_009_4.0_image.png" style="border: 0px solid ; width: 100%;" alt="" name="graphics8">
</p>
<p>The "Image" drop-down menu allows display of the
previous or next image in the series (but this is easier to perform
using the blue arrows displayed before the image name). <br>
</p>
<p>The "View" drop-down
menu allows the image to be displayed in different sizes (related by
scale factors of two), based on the image size and the resolution of
the monitor.</p>
<p>The "Settings" drop-down menu allows the colour of the predictions
to be changed (see <a href="#mozTocId286296" target="_blank">Indexing</a>
§5.2 for the default colours), and the size of the "Pick" box to be
changed. The third option (image summation) determines whether summed
images are calculated by addition or by taking the maximum or minimum
values. At present, only addition is implemented.<br>
</p>
<p>The line below allows selection of different images, either using
right and left blue arrow or selecting one from the drop-down list of
all
images in that sector. Alternatively the image number can be typed into
the "Go to" entry box. <br>
</p>
<p>For Pilatus and Eiger images only, the "Sum" entry box will allow
the display of the sum of several
images, the number (up to 20) can be chosen from the drop-down list.</p>
<p>The image being displayed can also be changed
by double-clicking on an image in the list shown in the "Images" pane of
the main iMosflm window. This will also re-active the image window if
it has been closed.<br>
</p>
<p><img src="images/img_010_4.0_histogram.png" name="graphics56" align="bottom" border="0" height="418" width="388">
</p>
<p>"+" and "-" will zoom the image without
changing the centre. The "Fit image" icon will restore the
image to its original size (right mouse button will have the same
effect). The "Contrast" icon will give a histogram of pixel
values. Use the mouse to drag the vertical dotted line, to the right
to lighten the image, to the left to darken it. Try adjusting the
contrast. The "Lattice" entry window can be used when processing images
with multiple lattices present, see <a href="#mozTocId189423">multiple
lattices</a> §5.3.</p>
<p>The "reverse video" icon allows an image to be rendered as light
spots on a dark background that can help visualise small diffraction
spots (e.g. for data collected using a Pilatus or Eiger detector).<br>
</p>
<h2><a class="mozTocH2" name="mozTocId114918"></a><font face="Times New Roman, serif"><font size="4"><b>4.1
Display Icons</b></font></font></h2>
<p><img style="width: 645px; height: 29px;" alt="" src="images/img_011_4.1_icons.png"></p>
<p>
The eight icons on the left, control the display of the direct
beam position (magenta cross), spots
found for indexing, bad spots, predicted reflections, masked
areas, spot-finding search area, resolution limits and display of the
active mask for Rigaku detectors respectively. Clicking on these items
will turn their display on or off.<br>
</p>
<p>These are followed by icons for Zoom, Pan and Selection tools, and
tools for adding spots manually (for indexing), defining masks, circle
fitting and erasing spots or masks (the pink eraser). The final icon
allows the phi profile of a reflection to be displayed (see <a href="#mozTocId431248">§5.6.2</a>).</p>
<p>Next on this toolbar are the entry boxes for <i>h, k</i> & <i>l</i> indices for a reflection. If this reflection is present among
the predicted spots for this image, a green tick will be displayed in
the button following the entry boxes, and a large X will be drawn over
that reflection in the display. If it is not present a red exclamation
mark will be displayed (as above).The final
icon relates to processing images with multiple lattices, (see <a href="#mozTocId189423" target="_blank">multiple lattices</a> §5.3)
and is not described here.<br>
</p>
<h3><a class="mozTocH3" name="mozTocId74027"></a><font face="Times New Roman, serif"><font size="3"><b>4.1.1
Masked areas - circular backstop shadow</b></font></font></h3>
<img style="width: 642px; height: 28px;" alt="" src="images/img_012_4.1.1_maskareaicon.png"><br>
<br>
<em>Select
the masked area icon.</em> A green circle will be displayed showing
the default position and size of the backstop shadow.
<p><img style="width: 642px; height: 27px;" alt="" src="images/img_013_4.1.1_zoomicon.png"><br>
</p>
<p><em>Make
sure that the Zoom icon (magnifying glass) is selected and use the
left-mouse-button (abbreviated to LMB in following text) to drag out
a rectangle around the centre of the image.</em> The inner dotted
yellow rectangle will show the part of the image that will actually
appear in the zoomed area.</p>
<p><img src="images/img_014_4.1.1_backstop.png" name="graphics12" align="bottom" border="0" height="323" width="327">
</p>
<p><img style="width: 642px; height: 28px;" alt="" src="images/img_015_4.1.1_pointer.png"><br>
</p>
<p>
<em>Choose
the Selection Tool.</em> When placed over the perimeter of the
circle, the radius of the circular backstop shadow will be displayed.
<em>Use the LMB to drag the circle to increase its diameter to that
of the actual shadow on the image.</em> The position of the circle
can be adjusted with LMB placed on the cross that appears in the
centre of the green circle. <em>Adjust the size and position of the
circle so that it matches the shadow.</em></p>
<h3><a class="mozTocH3" name="mozTocId23713"></a><font face="Times New Roman, serif"><font size="3"><b>4.1.2
Masked areas - general exclusions</b></font></font></h3>
<img style="width: 642px; height: 28px;" alt="" src="images/img_016_4.1.2_maskicon.png"><br>
<em>Choose the Masking tool</em>. Any existing masked areas will
automatically be displayed. <em>Use LMB to define the four corners of
the region to be masked.</em> When the fourth position is given, the
masked region will be shaded. This region will be excluded from spot
finding and integration. This provides a powerful way of dealing with
backstop shadows (note that multiple masks can be defined). To modify
an existing mask, choose the Selection tool
and use the LMB to drag any of the four vertices to a new position.
<p>To delete a mask, choose the Spot and mask eraser tool. Place the
mouse anywhere within the shaded masked area, and use LMB to delete
the mask. <em>Delete any masks that you have created.<br>
<img style="width: 642px; height: 28px;" alt="" src="images/img_017_4.1.2_rubbericon.png"><br>
</em></p>
<h3><a class="mozTocH3" name="mozTocId209370"></a><font face="Times New Roman, serif"><font size="3"><b>4.1.3 Spot
search area</b></font></font></h3>
<p><em><img style="width: 644px; height: 28px;" alt="" src="images/img_018a_4.1.3_spotsearchicon.png"><br>
</em></p>
<p><em>Select the Show spotfinding search area icon.</em> The inner
and outer radii for the spot search will be displayed as shown below.
If the images are very weak, the spot finding radius will
automatically be reduced (this behaviour can be changed using the
Settings -> Processing options -> Spot finding -> Automatic
Resolution reduction tickbox), but this provides additional control
over the area to be searched.</p>
<p>Either can be changed by dragging with the LMB. <em>Do not change
the radii for these images.</em></p>
<p><img src="images/img_018_4.1.3_spotsearch.png" name="graphics16" align="bottom" border="0" height="471" width="439">
</p>
<p><br>
<br>
</p>
<table border="1" bordercolor="#ff0000" cellpadding="2" cellspacing="3">
<tbody>
<tr>
<td>
<p><b>Advanced Usage</b></p>
<p>The red rectangle displays the area used to determine an
initial estimate of the background of the image. It is important that
this does not overlap significant shadows on the image. It can be
shifted laterally or changed in orientation (in 90° steps) by dragging
with the LMB.</p>
</td>
</tr>
</tbody>
</table>
<h3><a class="mozTocH3" name="mozTocId890852"></a><font face="Times New Roman, serif"><font size="3"><b>4.1.4
Resolution limits</b></font></font></h3>
<img style="width: 642px; height: 28px;" alt="" src="images/img_019_4.1.4_resolutionicon.png"><br>
<em>Select the Show resolution limits icon.</em> The circular low
and high
resolution limits will be displayed. The resolution limits can be
changed by dragging the perimeter of the circle with LMB (make sure
that the Selection Tool has been chosen). The resolution limits will
affect Strategy, Cell refinement and Integration, but not spot
finding or indexing. The low resolution is not strictly correct (it
falls within the backstop shadow) but does not need to be changed
because spots within the backstop shadow will be rejected.
<p><img src="images/img_020_4.1.4_resolutionimg.png" name="graphics55" align="bottom" border="0" height="517" width="600"></p>
<h3><a class="mozTocH3" name="mozTocId746242"></a><font face="Times New Roman, serif"><font size="3"><b>4.1.5 Zooming
and Panning</b></font></font></h3>
<em>
First
select a region of the image to be zoomed with the Zoom tool.<br>
<br>
</em><img style="width: 642px; height: 28px;" alt="" src="images/img_021_4.1.5_panicon.png"><br>
<span style="font-style: italic;">Select the Pan tool and pan the
displayed area by holding down LMB
and moving the mouse. </span><br>
<h3><a class="mozTocH3" name="mozTocId310974"></a><font face="Times New Roman, serif"><font size="3"><b>4.1.6
<span style="font-family: Times New Roman,Times,serif;">Circle fitting</span></b></font></font></h3>
<p>The circle fitting tool can be used to determine the direct beam
position by fitting a circle to a set of points on a powder
diffraction ring on the image (typically due to icing) or to fit a
circular backstop shadow (although using the masking tool is probably
easier).</p>
<p><img style="width: 641px; height: 27px;" alt="" src="images/img_022_4.1.6_circleicon.png"><br>
</p>
<p><em>Select the circle fitting tool. Three new icons will appear in
the image display area. There are two (faint) ice rings visible on
the image at 3.91Å and 3.67Å. Click with LMB on several positions
(6-8) on the outer ring (as it is slightly stronger). Then click on
the top circular icon.</em></p>
<p>A circle that best fits the selected points (displayed as yellow
crosses) will be drawn, and the direct beam position at the centre of
this circle will be indicated with a green cross. The direct beam
coordinates will be updated to reflect this new position.</p>
<p><img src="images/img_023_4.1.6_circleimg.png" style="border: 0px solid ; width: 100%;" alt="" name="graphics20">
</p>
<h3 style="font-family: Times New Roman,Times,serif;"><a class="mozTocH3" name="mozTocId822853"></a><small>4.1.7 Phi
profile</small></h3>
<img style="width: 642px; height: 27px;" alt="" src="images/img_023a_4.1.7_phiprofileicon.png"><br>
<br>
For version 7.4.0 onwards, the phi profile of individual reflections
can be plotted using the "Phi profile" icon. More details can be found
in section <a href="#mozTocId431248">5.6.2</a><br>
<h1><a class="mozTocH1" name="mozTocId150573"></a><font face="Times New Roman, serif">5. Spot
finding, indexing and mosaicity estimation</font></h1>
<p>When images have been added to the session, the "Indexing" operation
becomes accessible (it is no longer greyed-out).</p>
<p><em>Click on Indexing.</em> This will bring up the major Indexing
window in place of the Images window.</p>
<h2><a class="mozTocH2" name="mozTocId591049"></a><font face="Times New Roman, serif"><font size="4"><b>5.1
Spot Finding</b></font></font></h2>
<p>By default, the first image and a second image 90° away in phi (or
as close to 90°
as possible) will be selected and a spot search carried out on both
images (This
is controlled by the "Automatically find spots on entering
Autoindexing" tick box in the Spot finding tab of Processing options).</p>
<p>Found spots will be displayed as crosses in the Image Display window
(red for those above the intensity threshold, yellow for those below).
Only those above the threshold will be used in indexing. The intensity
threshold normally defaults to 20, but will be automatically
reduced to 10 or 5 for weak images. The threshold is determined by the
last
image to be processed.</p>
<p><img src="images/img_024_5.1_indexspots.png" name="graphics57" align="bottom" border="0" height="143" width="746">
</p>
<p><br>
<br>
</p>
<p>The number of spots found, together with any manual additions or
deletions, are also given.</p>
<p>Images to be searched for spots can be specified in several ways:</p>
<ol>
<li>
<p style="background: transparent url(none) repeat scroll 0% 50%; margin-bottom: 0cm; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">Simply
type in the numbers of the images (e.g. 1, 84 above).</p>
</li>
<li>
<p style="background: transparent url(none) repeat scroll 0% 50%; margin-bottom: 0cm; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">Use
the "Pick first image" icon (single blue circle).</p>
</li>
<li>
<p style="background: transparent url(none) repeat scroll 0% 50%; margin-bottom: 0cm; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">Use
the "Pick two images ~90 apart" icon (two blue circles) . This is the
default behaviour.</p>
</li>
<li>
<p style="background: transparent url(none) repeat scroll 0% 50%; margin-bottom: 0cm; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">Use
the "Select images ..." icon (multiple circles). If selected, all
images in the sector are displayed in a drop-down list. Click on a
image to select it, then double-click on the search icon (resembling a
target, in the colum headed "Find") for that image to run the spot
search. The image will move to the top of the list (together with other
images that have been searched).</p>
</li>
</ol>
<p>Images to be used for indexing can be selected from those that
have been searched by clicking on the "Use" button. If this
box was previously checked, then clicking will remove this image from
those to be used for indexing. It can be added again by clicking the
"Select images ..." icon and clicking on the "Use"
box.</p>
<p><span style="font-weight: bold;">Before indexing, always check by
looking at the image display that the spot finding has worked
correctly, ie that most spots that you can see have been found, that
multiple crosses have not been drawn over the same spot, that spots
have not been placed over ice rings or ice spots. Check all images that
will be used in indexing.</span><br>
</p>
<h3><a class="mozTocH3" name="mozTocId495561"></a><font face="Times New Roman, serif"><font size="3"><b>5.1.1
If the spot finding has not worked well<br>
</b></font></font></h3>
<p>It is possible to get more details on the spot finding and these can
be useful in deciding which parameters to change in the spot search.
Use LMB to select an image used in spot finding, the line will be
highlighted, then use right mouse button to bring up a "Details"
button. <br>
</p>
<p><img style="width: 709px; height: 67px;" alt="" src="images/img_024a_5.1.1_detailsbutton.png"><br>
</p>
<p><br>
Clicking with LMB on "Details" will pop up a window giving the spot
search results for this image.<br>
</p>
<p><img style="width: 749px; height: 387px;" alt="" src="images/img_024b_5.1.1_spotresults.png"><br>
</p>
<p>In this case there are a very large number of spots rejected as
having too few pixels. While many of these are probably not real spots,
it suggests that reducing the minimum number of pixels (30 in this