Author: bugman
Date: Fri Mar 16 18:26:54 2012
New Revision: 15529
URL: http://svn.gna.org/viewcvs/relax?rev=15529&view=rev
Log:
Shifted the screenshots into its own webpage
http://www.nmr-relax.com/screenshots.html.
The screenshots were originally part of the
http://www.nmr-relax.com/features.html page, but are now
separated. The http://www.nmr-relax.com/screenshots.html page has been also
added to the side menu.
Added:
website/screenshots.html
- copied, changed from r15526, website/features.html
Modified:
website/features.html
website/menu.html
Modified: website/features.html
URL:
http://svn.gna.org/viewcvs/relax/website/features.html?rev=15529&r1=15528&r2=15529&view=diff
==============================================================================
--- website/features.html (original)
+++ website/features.html Fri Mar 16 18:26:54 2012
@@ -116,61 +116,8 @@
<h3>relax GUI</h3>
<p>To start relax with the graphical interface, type:</p>
<p><em>$ relax -g</em></p>
+ <p>Some <a href="screenshots.html">screenshots</a> of the GUI in action
are available.</p>
- <h4>Screenshots</h4>
- <p>Some screenshots of the second version of the GUI (for the relax
1.3.14 release) are:</p>
-
- <table class="screenshot_table">
- <tr>
- <td>
- <a href="images/screenshots/full/start.png"><img
src="images/screenshots/small/start.png" alt="Screenshot: Blank
GUI."/></a><br/>relax starting interface
- </td>
- <td>
- <a href="images/screenshots/full/analysis_wizard.png"><img
src="images/screenshots/small/analysis_wizard.png" alt="Screenshot: Analysis
wizard."/></a><br/>The analysis selection wizard
- </td>
- <td>
- <a href="images/screenshots/full/analysis_noe.png"><img
src="images/screenshots/small/analysis_noe.png" alt="Screenshot: Steady-state
NOE tab."/></a><br/>Steady-state NOE analysis
- </td>
- </tr>
- <tr>
- <td>
- <a href="images/screenshots/full/analysis_r1.png"><img
src="images/screenshots/small/analysis_r1.png" alt="Screenshot: R1
tab."/></a><br/>R<sub>1</sub> analysis
- </td>
- <td>
- <a href="images/screenshots/full/analysis_r2.png"><img
src="images/screenshots/small/analysis_r2.png" alt="Screenshot: R2
tab."/></a><br/>R<sub>2</sub> analysis
- </td>
- <td>
- <a href="images/screenshots/full/analysis_mf.png"><img
src="images/screenshots/small/analysis_mf.png" alt="Screenshot: Model-free
tab."/></a><br/>Model-free analysis
- </td>
- </tr>
- <tr>
- <td>
- <a href="images/screenshots/full/relax_controller.png"><img
src="images/screenshots/small/relax_controller.png" alt="Screenshot: relax
controller."/></a><br/>The relax controller
- </td>
- <td>
- <a href="images/screenshots/full/spin_viewer.png"><img
src="images/screenshots/small/spin_viewer.png" alt="Screenshot: Spin viewer
window."/></a><br/>Spin viewer window
- </td>
- <td>
- <a href="images/screenshots/full/results_viewer.png"><img
src="images/screenshots/small/results_viewer.png" alt="Screenshot: Results
viewer window."/></a><br/>Results viewer window
- </td>
- </tr>
- <tr>
- <td>
- <a href="images/screenshots/full/pipe_editor.png"><img
src="images/screenshots/small/pipe_editor.png" alt="Screenshot: Pipe editor
window."/></a><br/>Pipe editor window
- </td>
- <td>
- <a href="images/screenshots/full/relax_prompt.png"><img
src="images/screenshots/small/relax_prompt.png" alt="Screenshot: relax prompt
window."/></a><br/>relax prompt window
- </td>
- <td>
- <a href="images/screenshots/full/about_gui.png"><img
src="images/screenshots/small/about_gui.png" alt="Screenshot: About GUI
screen."/></a><br/>About GUI screen
- </td>
- </tr>
- <tr>
- <td>
- <a href="images/screenshots/full/about_relax.png"><img
src="images/screenshots/small/about_relax.png" alt="Screenshot: About relax
screen."/></a><br/>About relax screen
- </td>
- </tr>
- </table>
</div>
</div>
Modified: website/menu.html
URL:
http://svn.gna.org/viewcvs/relax/website/menu.html?rev=15529&r1=15528&r2=15529&view=diff
==============================================================================
--- website/menu.html (original)
+++ website/menu.html Fri Mar 16 18:26:54 2012
@@ -9,12 +9,13 @@
<li class="menu_def"><a href="docs.html" title="The internal help
system, sample scripts, and the relax manual">Documentation</a></li>
<li class="menu_def"><a href="download.html" title="Instructions for
downloading relax">Download</a></li>
<li class="menu_def"><a href="communication.html" title="The bug tracker
and mailing lists">Communication</a></li>
+ <li class="menu_def"><a href="api/" title="The relax internals">API
documentation</a></li>
+ <li class="menu_def"><a href="devel_platform.html" title="Setting up a
development platform">Development platform setup</a></li>
+ <li class="menu_def"><a href="faq.html" title="Frequently asked
questions (FAQ)">relax FAQ</a></li>
+ <li class="menu_def"><a href="screenshots.html" title="relax GUI
screenshots">Screenshots</a></li>
<li class="menu_def"><a href="events.html" title="The material related
to events publicizing relax">Events</a></li>
<li class="menu_def"><a href="refs.html" title="References for
relax">References</a></li>
<li class="menu_def"><a href="links.html" title="Where to find relax on
the web">Links</a></li>
- <li class="menu_def"><a href="api/" title="The relax internals">API
documentation</a></li>
- <li class="menu_def"><a href="devel_platform.html" title="Setting up a
development platform">Development platform setup</a></li>
- <li class="menu_def"><a href="faq.html" title="Frequently asked
questions (FAQ)">relax FAQ</a></li>
<li class="menu_title">relax @ Gna!</li>
<li class="menu_def"><a href="http://gna.org/projects/relax"; title="The
Gna! site for the project relax.">The relax project</a></li>
Copied: website/screenshots.html (from r15526, website/features.html)
URL:
http://svn.gna.org/viewcvs/relax/website/screenshots.html?p2=website/screenshots.html&p1=website/features.html&r1=15526&r2=15529&rev=15529&view=diff
==============================================================================
--- website/features.html (original)
+++ website/screenshots.html Fri Mar 16 18:26:54 2012
@@ -25,99 +25,9 @@
<div class="main">
<div class="main_box">
- <h1>Program features</h1>
+ <h1>Screenshots</h1>
- <p></p>
-
- <div class="main_h2" id="primary_refs">
- <h2>Literature</h2>
- <p>The primary references for the program relax are <a
href="refs.html#dAuvergneGooley08a">d'Auvergne and Gooley, 2008a</a> and <a
href="refs.html#dAuvergneGooley08b">d'Auvergne and Gooley, 2008b</a>.</p>
-
- <p>Other literature related to the improved model-free analysis used
within relax, which can nevertheless be applied to other techniques, include
model-free model selection (<a href="refs.html#dAuvergneGooley03">d'Auvergne
and Gooley, 2003</a>; <a href="refs.html#Chen04">Chen et al., 2004</a>),
model-free model elimination (<a
href="refs.html#dAuvergneGooley06">d'Auvergne and Gooley, 2006</a>), the
theory (<a href="refs.html#dAuvergneGooley07">d'Auvergne and Gooley,
2007</a>) behind the new model-free optimisation protocol (<a
href="refs.html#dAuvergneGooley08b">d'Auvergne and Gooley, 2008b</a>), and
the hybridisation of different models (<a href="refs.html#Horne07">Horne et
al., 2007</a>; <a href="refs.html#dAuvergneGooley08b">d'Auvergne and Gooley,
2008b</a>). Most of these details can be found in the PhD thesis of <a
href="refs.html#dAuvergne06">d'Auvergne, 2006</a>.</p>
-
-
- </div>
-
- <div class="main_h2" id="theories">
- <h2>Supported NMR theories</h2>
- <p>The following NMR relaxation data analysis techniques are currently
supported by relax:</p>
-
- <ul>
- <li>Model-free analysis (<a href="refs.html#LipariSzabo82a">Lipari and
Szabo, 1982a</a>; <a href="refs.html#LipariSzabo82a">Lipari and Szabo,
1982b</a>; <a href="refs.html#Clore90">Clore et al., 1990</a>)</li>
- <li>Reduced spectral density mapping (<a
href="refs.html#Farrow95">Farrow et al., 1995</a>, <a
href="refs.html#Lefevre96">Lefevre et al., 1996</a>)</li>
- <li>Consistency testing - the validation of multiple field NMR
relaxation data (<a href="refs.html#Morin09">Morin and Gagné,
2009</a>)</li>
- <li>Exponential curve fitting (to find the R<sub>1</sub> and
R<sub>2</sub> NMR relaxation rates)</li>
- <li>Steady-state NOE calculation</li>
- <li>Determination of absolute stereochemistry of flexible molecules
(using isotropic and anisotropic NMR parameters (NOE, ROE, and RDC) combined
with MD simulation or simulated annealing, and ORD)</li>
- <li>The N-state model for investigating domain motions</li>
- <li>The frame order theory</li>
- <li>Conformational analysis of paramagnetically tagged sugars</li>
- <li>Analysis of RDCs and PCSs using ensemble of structures (the N-state
model of dynamics)</li>
- </ul>
-
- </div>
-
- <div class="main_h2" id="tools">
- <h2>Data analysis tools</h2>
- <p>The following tools are implemented as modular components to be used
by any data analysis technique:</p>
-
- <ul>
- <li>Numerous high-precision optimisation algorithms</li>
- <li>Model selection (<a href="refs.html#dAuvergneGooley03">d'Auvergne
and Gooley, 2003</a>; <a href="refs.html#Chen04">Chen et al., 2004</a>)
- <ul>
- <li>Akaike's Information Criteria (AIC)</li>
- <li>Small sample size corrected AIC (AICc)</li>
- <li>Bayesian or Schwarz Information Criteria (BIC)</li>
- <li>Bootstrap model selection</li>
- <li>Single-item-out cross-validation (CV)</li>
- <li>Hypothesis testing ANOVA model selection (only the model-free
specific technique of <a href="refs.html#Mandel95">Mandel et al., 1995</a> is
supported)</li>
- </ul></li>
- <li>Monte Carlo simulations (error analysis for all data analysis
techniques)</li>
- <li>Model elimination - the removal of failed models prior to model
selection (<a href="refs.html#dAuvergneGooley06">d'Auvergne and Gooley,
2006</a>)</li>
- </ul>
-
- </div>
-
- <div class="main_h2" id="vis">
- <h2>Data visualisation</h2>
- <p>The results of an analysis, or any data input into relax, can be
visualised using a number of programs:</p>
-
- <ul>
- <li><a href="http://hugin.ethz.ch/wuthrich/software/molmol/";>MOLMOL</a>
- 1D data can be mapped onto a structure either by the creation of MOLMOL
macros or by direct control of the program.</li>
- <li><a href="http://www.pymol.org/";>PyMOL</a> - visualisation of
diffusion tensors and cone models by using the software as a Python
package.</li>
- <li><a href="http://plasma-gate.weizmann.ac.il/Grace";>Grace</a> - any
2D data can be plotted.</li>
- <li><a href="http://www.opendx.org";>OpenDX</a> - The chi-squared space
of models with three parameters can be mapped and 3D images of the space
produced.</li>
- </ul>
- </div>
-
- <div class="main_h2" id="interface">
- <h2>Interfacing with other programs</h2>
- <p>relax can create the input files, execute in-line, and then read the
output of the following programs. These programs can be
-used as optimisation engines replacing the minimisation algorithms built
into relax:</p>
-
- <ul>
- <li><a href="http://www.nmr.ru/dasha.html";>Dasha</a> (model-free
analysis)</li>
- <li><a
href="http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer";>Modelfree</a>
(model-free analysis)</li>
- </ul>
- </div>
-
- <div class="main_h2" id="UI">
- <h2>The user interfaces (UI)</h2>
- <p>relax can be used through the following UIs:</p>
-
- <ul>
- <li>The prompt - this is the primary interface of relax. Rather than
reinventing a new command language, relax's interface is the powerful Python
prompt. This gives the power user full access to a proven programming
language.</li>
- <li>Scripting - this provides a more powerful and flexible framework
for controlling the program. The script will be executed as Python code
enabling advanced programming for automating data analysis. All the features
available within the prompt environment are accessible to the script.</li>
- <li>Graphical User Interface (GUI) - this offers a simple and easy way
of performing data analysis. Calculation of steady-state NOE, curve fitting
of R<sub>1</sub> and R<sub>2</sub> NMR relaxation rates as well as model-free
analysis are supported. Most parameters used for analysis can be set
manually, but system standards are set accoring to <a
href="refs.html#dAuvergneGooley08b">d'Auvergne and Gooley, 2008b</a>. In
addition, the graphical user interface has a fully automated model-free
analysis feature that performs analysis without any user intervention after
loading NOE, R<sub>1</sub> and R<sub>2</sub> data.</li>
- </ul>
-
- <p>The primary references for relax and the UIs are <a
href="refs.html#dAuvergneGooley08a">d'Auvergne and Gooley, 2008a</a> and <a
href="refs.html#dAuvergneGooley08b">d'Auvergne and Gooley, 2008b</a>, whereas
the primary reference for the GUI is <a href="refs.html#Bieri11">Bieri et
al., 2011</a>.</p>
-
- <h3>relax GUI</h3>
- <p>To start relax with the graphical interface, type:</p>
- <p><em>$ relax -g</em></p>
-
- <h4>Screenshots</h4>
+ <h2>GUI screenshots</h2>
<p>Some screenshots of the second version of the GUI (for the relax
1.3.14 release) are:</p>
<table class="screenshot_table">
r15529 - in /website: features.html menu.html screenshots.html