An introduction to 3dmod, the image display and modeling program in IMOD, is now a separate document.
There is also a reference guide that gives a description of each IMOD program and a link to its man page.
csh -f imod_3.11.2_FC2.cshcsh -f imod_3.11.2_FC2.csh -dir /optcsh -f imod_3.11.2_FC2.csh -extract
IMODtempDir. There are two other
useful options: -script to install
startup scripts to a different location, and -skip to
skip installing startup scripts. Use:csh -f imod_3.11.2_FC2.csh -help
Processor: Almost any Intel or AMD processor from the last 5
years will run adequately
Video Card: any relatively modern Nvidia card (GeForce or Quadro, 64 MB
or higher cards preferred)
Minimum memory size: 512MB
Minimum disk size: 15 GB
Operating System: Red Hat Workstation 4 or Fedora 4 or higher
Nvidia Linux device drivers and OpenGL libraries from Nvidia, at least version 8776 or
higher due to security concerns
Nvidia installation. Installing Nvidia drivers is now fairly straightforward except under Fedora Core 6, but here are some instructions that may be helpful. The latest versions of the drivers change the Driver line in /etc/X11/xorg.conf from "nv" to "nvidia" if you accept their offer to modify the file. In addition, here is a sample of a /etc/X11/xorg.conf file from Fedora Core 4, set up to use an old 24-inch Sony monitor.
Compatibility packages for Fedora Core 4 or higher. One or two packages not in the default installation are needed to run IMOD under a fresh installation of FC4 on up. If you are running a version of IMOD built under FC4, you need compat-libf2c. The reason for this is that the Fortran compiler g77 has been declared "legacy" even though its successor, gfortran, is too buggy to rely on yet. To install this, use:
sudo yum install 'compat-libf2c-*'libg2c.so is not
available (such as on Suse 10.3), then add the -libg2c
option to the command line when you install IMOD, and a copy of this
library inside IMOD will be used if it is available in the package that
you are installing from.If you are running an IMOD built under FC2, you also need compat-libstdc++-33, which you can install with:
sudo yum install compat-libstdc++-33
Window manager settings. To keep 3dmod from bogging down when it is displaying complex models, the window manager can be set to display only the outline and not the contents of windows when they are moved or resized. This cannot be done under Gnome but it can under KDE, by opening up the Control Center and selecting "Look and Feel" or "Desktop" (depending on KDE version), then "Window Behavior" then the "Moving" panel.
The self-installing package will install to a directory named IMOD
under /usr/local
unless given an alternate location to /usr/local with the
-dir
option. It will copy IMOD-linux.sh and IMOD-linux.csh
to /etc/profile.d. unless given an alternate
location with the -script option or told to skip this
step with the -skip option. To accomplish all
of this, change directory to the place where the package is located and
enter, for example:
sudo csh -f
imod_3.11.2_FC2.csh
You will have to open a new window, or possibly even log out and
log back in, for the installation to take effect.
/etc/cshrc,
/usr/local/etc/cshrc,
or users' .cshrc, .bashrc, or .bash_profile
files. The advantage of the current procedure is that future
upgrades
will be easier, especially if the startup files change..cshrc
files of individual users of tcsh (where <location of
IMOD> is the absolute path to the IMOD directory):setenv IMOD_DIR <location of IMOD>if (-e $IMOD_DIR/IMOD-linux.csh) source
$IMOD_DIR/IMOD-linux.csh .bash_profile of
individual
users under bash:export IMOD_DIR=<location of IMOD>if [ -e $IMOD_DIR/IMOD-linux.sh ] ; then source
$IMOD_DIR/IMOD-linux.sh ; fi.cshrc or .bash_profile,
you would place these commands in the system-wide startup
scripts. You should always source the startup script that comes
with an IMOD distribution, not make a copy of the startup script and
incorporate it into other scripts.To install manually from the tar file, do the following steps
after running the self-installing file with the -extract
option:
mv imod_3.11.2_FC2.tar.gz /usr/local cd /usr/local tar -xzf imod_3.11.2_FC2.tar.gz ls -l IMOD -> imod_2.7.6), then enter rm IMOD mv IMOD oldIMOD ln -s imod_3.11.2 IMOD cp IMOD/IMOD-linux.* /etc/profile.d tcsh,
enter:setenv IMOD_DIR `pwd`source IMOD-linux.csh 3dmod may fail to run if another
installed package has placed an incompatible Qt or OpenGL library on
your library load path. The sign of a problem with the Qt library
is an error message about an undefined symbol, usually a very long
string containing "QGLWidget". The remedy for these problems
depends on whether
your IMOD distribution has a Qt library included. IMOD-localQt.sh
and IMOD-localQt.csh in the top IMOD directory. Use
these to replace the startup files in /etc/profile.d:sudo cp IMOD-localQt.sh /etc/profile.d/IMOD-linux.sh
sudo cp IMOD-localQt.csh
/etc/profile.d/IMOD-linux.cshIMOD-qtconflict.sh and IMOD-qtconflict.csh,
that can be used to solve the problem. Try sourcing the
appropriate file, then try following the directions in the file and
sourcing it again. If this solves the problem, make any needed
changes to both files and copy them to /etc/profile.d,
without deleting IMOD-linux.*sh.
jre-1_5_0_06-linux-i586.bin
file
to /usr/local
sudo
mv jre-1_5_0_06-linux-i586.bin /usr/local
Next change your working directory to /usr/local
and execute the bin by entering
cd
/usr/local
sudo
sh
jre-1_5_0_06-linux-i586.bin
on the command line.
This will install the JRE in /usr/local/jre1.5.0_06.
The IMOD startup scripts assume that the JRE is in /usr/local/java,
so next create a link:
sudo
ln
-s jre1.5.0_06 java
If you upgrade to a different JRE, then you just
need to change the link. If you wish to use a different JRE than
the one pointed to by /usr/local/java, you must edit the IMOD-linux.sh
and IMOD-linux.csh scripts in /etc/profile.d
and define the variable IMOD_JAVADIR to specify the directory where the
JRE you wish to use is installed.
_osx_ppc
for a PowerPC (G4, G5, etc) or _osx_intel for an Intel
processor. The self-installing package will install to
/Applications or to
an alternate location with the -dir option. It will
not work by clicking on it, only by running it at the command
line. It will
place appropriate "source" commands for defining the user environment
in /etc/csh.login and
/etc/profile. You
need to be able to use sudo. Open a terminal window (under
Applications-Utilities), change
directory to the place where the package is located, and enter, e.g.:sudo csh -f imod_3.11.2_osx_ppc.csh/etc/csh.login (if
you
are
running tcsh) or /etc/profile (if you are running
bash).
If you are upgrading IMOD with the
default installation
procedures and your previous installation used another method of
setting environment variables, then you may need to remove "source" or
other environment-setting commands from various files, such as /etc/csh.login,
/etc/profile, or users' .cshrc, .bashrc,
or .profile files./usr/lib to
libraries
in the IMOD directories that will allow you to start 3dmod by clicking
on its icon. Run the linklibs-mac script by
entering: sudo $IMOD_DIR/linklibs-mac -i sudo $IMOD_DIR/linklibs-mac -u
If you are upgrading IMOD and have done this before, you
should run $IMOD_DIR/linklibs-mac -u before installing
the new version.-extract option, you have
two
alternatives. To do it from the command line, open a Terminal
window and:sudo mv imod_3.11.2_osx_ppc.tar.gz /Applicationscd /Applicationssudo tar xzf imod_3.11.2_osx_ppc.tar.gz ls -l IMOD -> imod_3.1.6), then enter sudo rm IMOD sudo mv IMOD oldIMOD sudo mv imod_3.11.2 IMODimod_3.11.2/etc/csh.login and /etc/profile,
unless they are already there from a previous installation of
IMOD. Use sudo to invoke emacs or pico on
these files, .e.g.: sudo emacs /etc/csh.loginIMOD/mac.cshrc to
the
end of /etc/csh.login, specifically the command if (-e /Applications/IMOD/IMOD-mac.csh) source
/Applications/IMOD/IMOD-mac.csh
Similarly, copy the text in IMOD/mac.bashrc to
the end of /etc/profile, specifically the command [ -r /Applications/IMOD/IMOD-mac.sh ] && source
/Applications/IMOD/IMOD-mac.sh/Applications/IMOD to
the name of the top IMOD directory in IMOD-mac.csh and IMOD-mac.sh and
in the source commands placed in /etc/csh.login and
/etc/profile. If you are sure you are not going to install
somewhere else in the future, you can avoid modifying IMOD-mac.csh
and IMOD-mac.sh by defining IMOD_DIR before the source
commands, i.e. with setenv IMOD_DIR <Location_of_IMOD>/etc/csh.login, or with export IMOD_DIR=<Location_of_IMOD>/etc/profile. 3dmod with
some keyboard modifiers, but this is painful. Just get a 3-button
mouse. It may just work when you plug it in, so try it in 3dmod
before installing drivers. Installing Logitech and some other
drivers may actually make it stop working, and the solution is to
uninstall the drivers.rxvt and a lightweight text
editor, nano (derived from pico and
similar
to the editor in the pine email program). You
can
upgrade a previous Cygwin installation using this package, using the
same procedure as described below.cygwinForIMOD.exe:setup.exe program and a cygwinMaster
folder with all the packages.setup.exeC:\cygwin unless you want
it
on a different disk. Do not install under a directory with spaces in
its name. In the rest of this document, C:\ is used in the examples,
and you need to substitute your location if it is different.cygwinMaster folder as the Local
Package DirectoryC:\cygwin. Terminal
windows and Cygwin programs such as the Unix tools will
display and work with paths that are relative to the Cygwin
installation. For example, if you have installed Cygwin in C:\cygwin
then the /usr/local/IMOD directory will exist in the
windows file systems as C:\cygwin\usr\local\IMOD./home (C:\cygwin\home)
and some bash
startup files are copied there.mkpasswd and mkgroup.
Do what it says, i.e. runmkpasswd -l > /etc/passwdmkgroup -l > /etc/group
rxvt one appear with
the traditional Cygwin icon, right-click on the shortcut to edit its
properties, and press the button to change the icon to select the
Cygwin icon. rxvt window is that you
can
copy and paste just like under Unix (highlight with left mouse button,
paste with middle mouse button). This capability uses the Windows
clipboard, so you can copy text in a Windows program (Ctrl-C) and paste
with the mouse in the rxvt window, or highlight in the rxvt
window
and paste in a Windows program with Ctrl-V. Another
advantage is that you can resize the rxvt window
horizontally as well as vertically. The cygwinMaster folder
contains two shortcuts and a configuration file that make it
easy to use rxvt. To use rxvt:Cygwin-bash.lnk or Cygwin-tcsh.lnk
from cygwinMaster to your desktop, depending on your
preferred shell.rxvt.Xdefaults from cygwinMaster
to your Cygwin home directory.rxvt.Xdefaults to .Xdefaults
(you cannot do this in Windows Explorer). .Xdefaults to adjust the font
size and default window size and location.Cygwin-bash or Cygwin-tcsh shortcut to Cygwin.rxvt.Xdefaults from the cygwinMaster
folder
to some other place where the users can access them (such as /usr/local).tcsh from the Shells
category. Be aware that changes in Cygwin periodically
break
something in IMOD. We try to keep up with these problems and
release updated packages of the current release version of IMOD, but it
is safer to use the package that we provide if it is adequate.IMOD-cygwin.sh and IMOD-cygwin.csh to
/etc/profile.d. It will not work by
clicking on it, only
by executing it from the command line. To
install IMOD, start a Cygwin terminal window, change to the
directory where the package is located, and enter, e.g.:csh imod_3.11.2_win.csh
IMOD_DIR
to be C:\cygwin\usr\local\IMOD HOME
to be C:\cygwin\home\usernamePATH, press "Edit", and
add C:\cygwin\bin; to the front of the path (the ";" is
a
separator).IMOD_DIR
as an environment variable in Windows as described above, but with the
appropriate letter instead of C, so that 3dmod will be
able to find help files if it is started by clicking on an icon.C:\cygwin\usr\local\IMOD\bin to the
Windows
path, in which case you will be able to run everything, including shell
scripts,
from a DOS window.CYGWIN to be nobinmode.
This will make command files from Setupcombine, but not
those from Copytomocoms, have DOS line endings.nda, mtk, mtoverlap),
you
can install ghostscript and
gsview for
Windows./usr/local
either from the command line or from an Explorer window, where the
location will appear as C:\cygwin\usr\local./usr/local and, if you have
an existing IMOD installed, rename it.cd /usr/local
mv IMOD oldIMODtar -xzf imod_3.11.2.tar.gz mv imod_3.11.2 IMOD cp IMOD/IMOD-cygwin.* /etc/profile.d.tar.gz distribution
instead of the self-installing distribution and use Winzip to
unpack it somewhere, (e.g., C:\Program Files), rename the
top directory to IMOD, and add the IMOD\bin directory
(e.g., C:\Program Files\IMOD\bin) to your path in
Windows, as described
above.
cpu.adoc file for enabling parallel
processing,
distortion correction files, noise files for microscope CTF correction,
and
local startup files.
The default
value for IMOD_CALIB_DIR is /usr/local/ImodCalib on all
platforms, and it is set in the IMOD startup scripts if it is not
already
defined. We have designed this directory as a place for local files
that
should not be replaced when IMOD is upgraded.
Minimally, then, you may want to create this directory and place a cpu.adoc
there defining the number of processors on one or more
machines. In addition, the IMOD startup scripts will try to source
local
startup scripts in this directory: IMOD-...csh will
source $IMOD_CALIB_DIR/IMOD.csh and IMOD-...sh
will source $IMOD_CALIB_DIR/IMOD.sh. You can use these
startup
scripts for
customizations, such as redefining IMOD_JAVADIR, instead
of
modifying the startup scripts that come with IMOD and get replaced with
each
new version. However, if you are going to take advantage of this
mechanism
and want to redefine IMOD_CALIB_DIR to point to a
different
location, your startup must set this environment variable before
sourcing the
IMOD startup scripts.
3dmod is the central graphical tool
of
the IMOD package. Beyond this, your initial problem may be getting
data into a format usable by the IMOD programs. If you are having
problems getting your data into a format usable by IMOD contact us for
help. 3dmod can read some common formats like JPEG,
TIFF, PNG, and BMP; it recognizes several specialized image formats
(DigitalMicrograph, EM, Hanspeter Winkler's NFF, PIF files from Bsoft);
and it has a dialog
box and options for specifying how to read raw data.
Use the program tif2mrc to
convert a series of TIFF image files into a single MRC image file. The tif2mrc
program has an option for converting 24-bit color to 8-bit grayscale
images, and options for dealing with unsigned 16 bit images, which are
a
potential problem because the standard MRC format supports only signed
16-bit
images. The following example will create a MRC file from a list of
TIFF files (cell01.tif, cell02.tif ...).
tif2mrc cell??.tif cell.mrc
See the tif2mrc manual page
for
more information on how to use tif2mrc.
newstack cell*.mrc cell.st raw2mrc, you need to know the
size of the images, the type of data, and the size of any header
information preceding the image. For example, if you have a set
of files (cell01.em, cell02.em, ...) with 1024 x 1024 images of signed
16-bit integers, and a header of 512 bytes, use:raw2mrc -t short -x 1024 -y 1024 -o 512 cell*.em cell.mrcIf the data need to have their bytes swapped because they come from a machine with the opposite byte ordering (e.g. PPC Mac versus Intel), use the -s option. If you do not know something about the image, such as the header size or whether the data are unsigned or need swapping, you may be able to figure it out just by trying different options for data types and swapping. If you do not know the header size, convert one file without the -o option, load it into 3dmod, and try to see where the image data start. If the final MRC image is upside down use the -f option in the initial conversion or use the program clip to flip the image back.
When 3dmod is started with an image file that it
does not recognize, it brings up a dialog that allows you to specify
the image and header size and the data type. Alternatively, you
can specify these features with options at the command line, which
could be the most convenient way to experiment and find the right
values. For example, the files in the previous command could be
displayed with:
3dmod -r 1024,1024,1 -H 512 -t 1 cell*.em
If you already have a 3-D model and wish to view it within
the IMOD model viewing program, 3dmodv, you will need to
convert the file into the IMOD format. See the IMOD model file
format ASCII and binary
specifications if you wish to write your own conversion program.
Model files from the HVEM3D program can be converted to the IMOD
model format using the rec2imod
program.
The IMOD model format can be either binary or ASCII. Currently supported machines can all read and write binary model files interchangeably, so the main use of the ASCII format would be to access the data for analysis or conversion by other programs. To convert a binary IMOD file (binary.imod) to an ASCII IMOD file (ascii.imod) use the imodinfo command :
imodinfo -a binary.imod > ascii.imod
or
imodinfo -a -f ascii.imod binary.imod
will both create an ASCII model file from the binary.imod model.
The ASCII format preserves many but not all possible features in the
model. It is moderately complex and may not be the most
convenient format to use for exporting or importing data. There
are also two programs, model2point
and point2model, that can be
used to convert an IMOD model to or from a simple list of point
coordinates.
eTomo
program. Conversely, the tilt series alignment procedures there
cannot be use dThere are three general methods for obtaining alignment transforms: manual adjustment of transformation parameters, solving for a transform from a set of fiducial points that correspond between two sections, and automated search for the best fit between two images.
Midas
can be used to create a transform list or to edit an existing list; it
can work with either "f" or "g" transform lists. To get a "g" transform
list from an "f" transform list use the xftoxg
program. xftoxg has options to leave long term trends in
the data, which are invoked by default when you run the program with
command-line arguments. Steps and Programs used in fiducial marker alignment.
3dmod : Creates a model in which points in each
contour
are placed on adjacent sections that mark the same area on both
sections. Note that a single contour corresponds to a single fiducial
marker, and the contour contains a point on each of the sections where
the marker appears. These are contours that pass between sections
rather than being confined to a single section. xfmodel : Creates a "f" transform list. xftoxg : Creates a "g" transform list, leaving
in
long term trends in the data. newstack : Creates an aligned image stack. Steps and programs used in automatic image alignment:
xfalign cell.mrc cell.xf xftoxg cell.xf
newstack -xform test.xg test.mrc newtest.mrc
If the automatic alignment is not always correct, it can be adjusted with the midas program. Start the program with:
midas test.mrc test.xf
A window will open up and you can view the alignment
between
any given pair of adjacent images. After making adjustments for any
sections that are out of alignment, save the transforms and exit the
program. Then rerun the xftoxg and newstack
commands shown above.
Note that newstack
and some of the other programs will not work with 24-bit color
images. Use the "-g" option to tif2mrc
to convert to gray scale when making the MRC stack. If you do
need to preserve the color information, then you can split the color
into three separate byte-mode files with the clip program, determine the alignment
with one color channel, apply the trasnformations to each of the 3
files separately, then merge the data again with clip.
For more background and explanation of the topics in this
section, see the guide to serial section
alignment.
Use the imodinfo command to get basic information from a model and print it out to a terminal or file. For example:
imodinfo cell.imod
# MODEL cell.imod
# NAME A little cell
# PIX SCALE: x = 1
# y = 1
# z = 9.17
# PIX SIZE = 0.00654
# UNITS: um
OBJECT 1
NAME: spindle pole
5 contours
object uses closed contours.
color (red, green, blue) = (0, 1, 1)
CONTOUR #1,2,0 16 points, length = 0.464513, area = 0.0134249
CONTOUR #2,2,0 14 points, length = 0.458311, area = 0.0125642
CONTOUR #3,2,0 8 points, length = 0.200755, area = 0.00277481
CONTOUR #4,2,0 13 points, length = 0.313501, area = 0.00664029
CONTOUR #5,2,0 9 points, length = 0.232374, area = 0.00272134
Total volume = 0.00228646
Total contour cylinder surface area = 0.10012.
Total mesh surface area = 0.0349499.
See also: Manual pages for 3dmodv,imodmesh, and imodinfo.