Leginon

h1. InstallationUpdate problems

* <link linkend="InstT_win_install">Python installer fails on pyScope and numExtension for

Windows</link>

* <link linkend="InstT_bad_update">Not all files are updated</link>

* <link linkend="InstT_1st_Grp">New Group/User added does not show up in the selection

list in Web Leginon Administration Tool</link>.

* <link linkend="Inst_no_tomo">I can't install SciPy/NumPy on SUSE</link>

* <link linkend="InstT_php_display_error">Something is not showing in Web viewer or the

administration tool components</link>

* <link linkend="instlT_updatecom">Stage does not move after a pyScope update on the

computer controlling the microscope</link>

h2. Failed pyScope numExtension Window installation through

python

<title>Why:</title>

*  Specially compiled pyScope and numExtension are needed to comunicate with Gatan

CCD camera. Currently we only have them compiled for python2.5

Solution: Download and use python2.5 and use the window-installer in win-install

folder (start by double-clicking them) not "python setup.py install".

h2. Incomplete Leginon update

This normally happens to files that you have modified in the previous version.

<title>Why:</title>

*  unknown

Solution: Remove the old installation first.

*  Find the location of your Leginon installation. Once you have tried,even

unsuccessfully, to install Leginon. You can use the following command to find

the directory:

<pre>Linux> cd

Linux> start-leginon.py -v</pre>

<pre>Window> Go to \All Programs\Leginon\Leginon Folder from your Start Menu</pre>

*  Go to the directory above it. This is normally the site-package directory

under your python installation

<pre>Linux> rm -r Leginon

Window> drag the Leginon folder to Recycle Bin</pre>

*  Redo Leginon installation.

h2. Installation without a class of nodes

If you encounter a problem with node classes that you don't actually use, you may avoid

loading the codes with the following modification:

*  Fnd the location of your Leginon installation

<pre>Linux> cd

Linux> start-leginon.py -v</pre>

*  go to the subdirectory of noderegistry

<pre>Linux/home> cd leginon_directory/noderegistry</pre>

*  edit the file "default.ncr" to coment out the registry of the class of nodes that

you do not need (Tomography node class in this example):

<pre>#[Tomography]

#module: tomography

#type: Pipeline

#package: tomography</pre>

h2. SciPy Installation failed in SuSE

SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK

package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from

http://repos.opensuse.org/science (need to specify your SuSE version and machine etc.

h2. Display errors on webviewer and web

administration tools

To display error and report them to get help for the php, including mysql-php and mrc

extension, do the following:

*  Find your php.ini the following parameters and change them accordingly:

<pre>display_errors = On

error_reporting  =  E_ALL &amp; ~E_NOTICE</pre>

*  Restart your apache server

<pre>> /etc/init.d/apache2 restart</pre>

*  From your webbrowser, refresh the problematic page. If you don't know what to do

with it, report it when you ask for help.