Frequently Asked Questions

Introduction

With the advent of a beta release of DNA 1.0.0, it has become evident that certain questions are asked repeatedly. This document should be a first port of call if you have a question, to see if you have a new question or an old one. A more appropraiate name may be frequently given answers.

Most questions come down to:

which means that if you have read the installation instructions you probably do have a proper question not a FAQ.

Things you need before you start

CCP4

The following things are needed before you start. If these things are not available the installation will not work. Firstly, you must have CCP4 5.0 or later installed, and have the "setup" script sourced so that typing

echo $CCP4

tells you where CCP4 is installed.

Python

The next thing that you need to have is a version of Python later than or equal to 2.3. You can tell if you have this by typing on a prompt:

graeme@ehtpx-pc1:~> python
Python 2.3.4 (#1, Jun 24 2004, 16:28:30)
[GCC 3.3.1 (SuSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
    

As you can see, I have version 2.3.4 which is fine. To exit the python shell type "Ctrl-D". If you do not have a suitable version of python, for instance you see:

[graeme@ehtpx-pc2 graeme]$ python
Python 2.2.1 (#1, Aug 30 2002, 12:15:30)
[GCC 3.2 20020822 (Red Hat Linux Rawhide 3.2-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
    

then you need to install a newer version of python. This is a straightforward process, but if you are not happy then ask whoever maintains your system to do this for you. Python is usually distributed as a source "tarball" which is available from http://www.python.org.

Java

The final thing that you absolutely need to have installed before you start is a recent Java SDK installation. You can test this by typing:

graeme@ehtpx-pc1:~> java -version
java version "1.4.2"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2-b28)
Java HotSpot(TM) Client VM (build 1.4.2-b28, mixed mode)
    

To get the version information and

graeme@ehtpx-pc1:~> which javac
/usr/lib/java/bin/javac
    

to see if you have the java compiler available. If you get these results then you are OK. Bad results look like this:

[graeme@ehtpx-pc2 graeme]$ java -version
java version "1.3.1"
jdkgcj 0.2.3 (http://www.arklinux.org/projects/jdkgcj)
gcj (GCC) 3.2 20020903 (Red Hat Linux 8.0 3.2-7)
Copyright (C) 2002 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[graeme@ehtpx-pc2 graeme]$ which javac
/usr/bin/javac
    

because this means that you don't have the Java 2 SDK from Sun installed. Installing java is a less straightforward process but there should be someone around who knows how to do this (a binary installer is available from http://java.sun.com).


./test_dna did not work

This is another common question. Firstly, ensure that the above section on versions has been read and satisfied - this is the most likely cause of problems. If you updated any versions of anything after installing dna (e.g. running release.sh) then you need to re-run release.sh to ensure that all of the components are correctly linked.

If you have reached this stage, then the next thing is to ensure that you have the correct environment set up. Type

echo ${DNAHOME}
    

You should seen an answer like

/home/graeme/dna-release
    

If you don't, then the environment is not properly set up. During the installation process a file named ~/dna_setup.sh was created. This includes all of the environment that DNA needs to work. If you are using the shell bash then type the following:

. ~/dna_setup,sh
    

Yes, that is "dot space twiddle slash" at the beginning. You can find out which shell you are using by typing

graeme@ehtpx-pc1:~> echo ${SHELL}
/bin/bash
    

If this is something like /usr/bin/csh or /usr/bin/tcsh then you will have to make a new "setup" file by copying ~/dna_setup.sh to ~/dna_setup.csh, then changing all of the instances of "export" to "setenv" and all of the instances of "=" to " ". Then type

source ~/dna_setup.csh
    

and you should be ok.

How do I set?

So, you have DNA working with the test data, and you want to really start using it - so you will probably want a set of user configurations. This is done by making a little XML file like this:

<?xml version="1.0" encoding="UTF-8"?>
<user_defaults>
    <default_values>
        <fileinfo>
            <directory>/media/backup/dna/dna-dev</directory>
            <prefix>screen1</prefix>
            <suffix>img</suffix>
            <run_number>1</run_number>
        </fileinfo>
        <oscillation_sequence>
            <start>1.0</start>
            <range>1.0</range>
            <number_of_images>2</number_of_images>
            <overlap>-89.0</overlap>
            <exposure_time>1.0</exposure_time>
            <start_image_number>1</start_image_number>
        </oscillation_sequence>
        <detector>
            <type>adsc</type>
        </detector>
        <beam>
            <x>81.0</x>
            <y>81.0</y>
        </beam>
        <resolution>1.5</resolution>
    </default_values>
    <index_parameters>
        <max_index_spot_rms_error>0.15</max_index_spot_rms_error>
        <max_beam_shift>0.1</max_beam_shift>
        <max_index_spot_frac_rejected>0.1</max_index_spot_frac_rejected>
        <min_threshold_I_sigma>10.0</min_threshold_I_sigma>
    </index_parameters>
    <strategy_parameters>
        <overlap_limit>2.0</overlap_limit>
    </strategy_parameters>
</user_defaults>
    

in ~/.dna/user_defaults.xml. This file must exist to do anything more than just ./test_dna - a real bug!

And finally...

If you have got this far, and read the release notes, and made all of the checks I have suggested, then you have a novel problem. Please feel free to get in touch on +44 1925 603228 or email me at g.winter@dl.ac.uk. I can also try and help with any of the above points.


Graeme Winter
Last modified: Fri Aug 20 13:17:53 BST 2004