Author: bugman
Date: Tue Oct 13 10:10:34 2015
New Revision: 28043
URL: http://svn.gna.org/viewcvs/relax?rev=28043&view=rev
Log:
Removed two old pages from the HTML manual at
http://www.nmr-relax.com/manual/index.html .
These are for the no longer existing frame_order.average_position and
frame_order.num_int_pts user
functions (the first was deleted, the second is now called
frame_order.sobol_setup).
Removed:
website/manual/frame_order_average_position.html
website/manual/frame_order_num_int_pts.html
Removed: website/manual/frame_order_average_position.html
URL:
http://svn.gna.org/viewcvs/relax/website/manual/frame_order_average_position.html?rev=28042&view=auto
==============================================================================
--- website/manual/frame_order_average_position.html (original)
+++ website/manual/frame_order_average_position.html (removed)
@@ -1,240 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.1//EN">
-
-<!--Converted with LaTeX2HTML 2008 (1.71)
-original version by: Nikos Drakos, CBLU, University of Leeds
-* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
-* with significant contributions from:
- Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
-<HTML>
-<HEAD>
-<TITLE>frame_order.average_position</TITLE>
-<META NAME="description" CONTENT="frame_order.average_position">
-<META NAME="keywords" CONTENT="relax">
-<META NAME="resource-type" CONTENT="document">
-<META NAME="distribution" CONTENT="global">
-
-<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=utf-8">
-
- <!--Google analytics JS-->
- <script type="text/javascript">
-
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-30096326-1']);
- _gaq.push(['_setDomainName', 'nmr-relax.com']);
- _gaq.push(['_trackPageview']);
-
- (function() {
- var ga = document.createElement('script'); ga.type =
'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' :
'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
- })();
-
- </script>
-
-<LINK REL="STYLESHEET" HREF="relax.css">
-
-<LINK REL="next" HREF="frame_order_num_int_pts.html">
-<LINK REL="previous" HREF="fix.html">
-<LINK REL="up" HREF="The_list_of_functions.html">
-<LINK REL="next" HREF="frame_order_num_int_pts.html">
-</HEAD>
-
-<BODY >
-
-<DIV CLASS="navigation"><!--Navigation Panel-->
-<A NAME="tex2html17086"
- HREF="frame_order_num_int_pts.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Next" ALIGN="BOTTOM" BORDER="0"
ALT="next" SRC="next.png"></A>
-<A NAME="tex2html17080"
- HREF="The_list_of_functions.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Up" ALIGN="BOTTOM" BORDER="0" ALT="up"
SRC="up.png"></A>
-<A NAME="tex2html17074"
- HREF="fix.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Previous" ALIGN="BOTTOM" BORDER="0"
ALT="previous" SRC="prev.png"></A>
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- HREF="Contents.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Contents" ALIGN="BOTTOM" BORDER="0"
ALT="contents" SRC="contents.png"></A>
-<A NAME="tex2html17084"
- HREF="Index.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Index" ALIGN="BOTTOM" BORDER="0"
ALT="index" SRC="index.png"></A> <A NAME="tex2html1"
- HREF="http://download.gna.org/relax/manual/relax.pdf";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/pdf_icon_nav.png";
- ALT="pdf_icon_nav.png"></A><A NAME="tex2html2"
- HREF="http://www.nmr-relax.com";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/relax_logo_nav.png";
- ALT="relax_logo_nav.png"></A>
-<BR>
-<B> Next:</B> <A NAME="tex2html17087"
- HREF="frame_order_num_int_pts.html">frame_order.num_int_pts</A>
-<B> Up:</B> <A NAME="tex2html17081"
- HREF="The_list_of_functions.html">The list of functions</A>
-<B> Previous:</B> <A NAME="tex2html17075"
- HREF="fix.html">fix</A>
- <B> <A NAME="tex2html17083"
- HREF="Contents.html">Contents</A></B>
- <B> <A NAME="tex2html17085"
- HREF="Index.html">Index</A></B>
-<BR>
-<BR></DIV>
-<!--End of Navigation Panel-->
-<!--Table of Child-Links-->
-<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
-
-<UL CLASS="ChildLinks">
-<LI><A NAME="tex2html17088"
-
HREF="frame_order_average_position.html#SECTION081244100000000000000">Synopsis</A>
-<LI><A NAME="tex2html17089"
-
HREF="frame_order_average_position.html#SECTION081244200000000000000">Defaults</A>
-<LI><A NAME="tex2html17090"
-
HREF="frame_order_average_position.html#SECTION081244300000000000000">Keyword
arguments</A>
-<LI><A NAME="tex2html17091"
-
HREF="frame_order_average_position.html#SECTION081244400000000000000">Description</A>
-<LI><A NAME="tex2html17092"
-
HREF="frame_order_average_position.html#SECTION081244500000000000000">Prompt
examples</A>
-</UL>
-<!--End of Table of Child-Links-->
-<HR>
-
-<H2><A NAME="SECTION081244000000000000000"></A> <A
NAME="uf:_frame_order.average_position"></A>
-<BR>
-frame_order.average_position
-</H2>
-<IMG
- WIDTH="128" HEIGHT="128" ALIGN="BOTTOM" BORDER="0"
- SRC="./frame_order.png"
- ALT="Image frame_order">
-
-<P>
-
-<H3><A NAME="SECTION081244100000000000000">
-Synopsis</A>
-</H3>
-
-<P>
-Define the mechanics of the average domain position.
-
-<P>
-
-<H3><A NAME="SECTION081244200000000000000">
-Defaults</A>
-</H3>
-
-<P>
-<DIV ALIGN="LEFT">
-<SPAN CLASS="textsf"><SPAN
CLASS="textbf">frame_order.average_position</SPAN>(pivot=`com',
translation=False)</SPAN>
-
-</DIV>
-
-<P>
-
-<H3><A NAME="SECTION081244300000000000000">
-Keyword arguments</A>
-</H3>
-
-<P>
- <SPAN CLASS="textsf">pivot:</SPAN> The type of pivot to use for the
rotation<A NAME="32487"></A> to the average domain position. This can be one
of `<TT>com</TT>' or `<TT>motional</TT>'.
-
-<P>
- <SPAN CLASS="textsf">translation:</SPAN> A flag specifying if the average
domain position should be allowed to translate during optimisation. If
False, then translation can be disabled.
-
-<P>
-
-<H3><A NAME="SECTION081244400000000000000">
-Description</A>
-</H3>
-
-<P>
-Prior to optimisation, the mechanics of the average moving domain position
must be specified. Having the domain shifted to the correct average position
is essential for understanding the dynamics as this information is the major
contributor to the RDC and PCS. The motional eigenframe (spherical or
Euler<A NAME="32493"></A> angles)<A NAME="32494"></A> and ordering (via
order<A NAME="32495"></A> parameters, cone angles<A NAME="32496"></A> or
torsion angles)<A NAME="32497"></A> come second, and are therefore severely
distorted by an incorrect average domain position.
-
-<P>
-There are two pieces of information affecting this average position - a
rotation<A NAME="32498"></A> and translation. For the rotation,<A
NAME="32499"></A> a pivot point is required. Note that this pivot is not
related to the pivot of the motions. However if you believe that your
starting structure lies within the uniform distribution of positions of the
domain motions, then the two pivots can be linked by setting the average
position pivot to the motional pivot. The default however is to set the
pivot to the centre of mass (CoM) of the moving domain.
-
-<P>
-The second option allows the average domain position to translate during
optimisation. By default, only a rotation<A NAME="32500"></A> of the initial
structure of the domain is rotated to the average position. But if the
rotation<A NAME="32501"></A> is not sufficient to shift the domain to the
average position, then a translation will be required. This option will be
ignored if no PDC data is present, as RDCs do not contain information about
the translation of the domain.
-
-<P>
-
-<H3><A NAME="SECTION081244500000000000000">
-Prompt examples</A>
-</H3>
-
-<P>
-To use the centre of mass as the rotational<A NAME="32503"></A> pivot and to
allow translation of the average domain position during optimisation, type
one of:
-
-<P>
-<PRE>[numbers=none]
-relax> frame_order.translate('com', True)
-</PRE>
-
-<P>
-<PRE>[numbers=none]
-relax> frame_order.translate(translation=True)
-</PRE>
-
-<P>
-<PRE>[numbers=none]
-relax> frame_order.translate(pivot='com', translation=True)
-</PRE>
-
-<P>
-To use the motional pivot as the average domain rotational<A
NAME="32510"></A> pivot while disallowing translation of, type one of:
-
-<P>
-<PRE>[numbers=none]
-relax> frame_order.translate('motional')
-</PRE>
-
-<P>
-<PRE>[numbers=none]
-relax> frame_order.translate('motional', False)
-</PRE>
-
-<P>
-<PRE>[numbers=none]
-relax> frame_order.translate(pivot='motional', translation=False)
-</PRE>
-
-<P>
-
-<BR>
-
-<DIV CLASS="navigation"><HR>
-<!--Navigation Panel-->
-<A NAME="tex2html17086"
- HREF="frame_order_num_int_pts.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Next" ALIGN="BOTTOM" BORDER="0"
ALT="next" SRC="next.png"></A>
-<A NAME="tex2html17080"
- HREF="The_list_of_functions.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Up" ALIGN="BOTTOM" BORDER="0" ALT="up"
SRC="up.png"></A>
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- HREF="fix.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Previous" ALIGN="BOTTOM" BORDER="0"
ALT="previous" SRC="prev.png"></A>
-<A NAME="tex2html17082"
- HREF="Contents.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Contents" ALIGN="BOTTOM" BORDER="0"
ALT="contents" SRC="contents.png"></A>
-<A NAME="tex2html17084"
- HREF="Index.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Index" ALIGN="BOTTOM" BORDER="0"
ALT="index" SRC="index.png"></A> <A NAME="tex2html1"
- HREF="http://download.gna.org/relax/manual/relax.pdf";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/pdf_icon_nav.png";
- ALT="pdf_icon_nav.png"></A><A NAME="tex2html2"
- HREF="http://www.nmr-relax.com";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/relax_logo_nav.png";
- ALT="relax_logo_nav.png"></A>
-<BR>
-<B> Next:</B> <A NAME="tex2html17087"
- HREF="frame_order_num_int_pts.html">frame_order.num_int_pts</A>
-<B> Up:</B> <A NAME="tex2html17081"
- HREF="The_list_of_functions.html">The list of functions</A>
-<B> Previous:</B> <A NAME="tex2html17075"
- HREF="fix.html">fix</A>
- <B> <A NAME="tex2html17083"
- HREF="Contents.html">Contents</A></B>
- <B> <A NAME="tex2html17085"
- HREF="Index.html">Index</A></B> </DIV>
-<!--End of Navigation Panel-->
-<ADDRESS>
-The <a href="http://www.nmr-relax.com";>relax</a> <a
href="http://www.nmr-relax.com/manual/";>user manual</a> (<a
href="http://download.gna.org/relax/manual/relax.pdf";>PDF</a>), created
2015-09-30.
-</ADDRESS>
-</BODY>
-</HTML>
Removed: website/manual/frame_order_num_int_pts.html
URL:
http://svn.gna.org/viewcvs/relax/website/manual/frame_order_num_int_pts.html?rev=28042&view=auto
==============================================================================
--- website/manual/frame_order_num_int_pts.html (original)
+++ website/manual/frame_order_num_int_pts.html (removed)
@@ -1,155 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.1//EN">
-
-<!--Converted with LaTeX2HTML 2008 (1.71)
-original version by: Nikos Drakos, CBLU, University of Leeds
-* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
-* with significant contributions from:
- Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
-<HTML>
-<HEAD>
-<TITLE>frame_order.num_int_pts</TITLE>
-<META NAME="description" CONTENT="frame_order.num_int_pts">
-<META NAME="keywords" CONTENT="relax">
-<META NAME="resource-type" CONTENT="document">
-<META NAME="distribution" CONTENT="global">
-
-<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=utf-8">
-
- <!--Google analytics JS-->
- <script type="text/javascript">
-
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-30096326-1']);
- _gaq.push(['_setDomainName', 'nmr-relax.com']);
- _gaq.push(['_trackPageview']);
-
- (function() {
- var ga = document.createElement('script'); ga.type =
'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' :
'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
- })();
-
- </script>
-
-<LINK REL="STYLESHEET" HREF="relax.css">
-
-<LINK REL="next" HREF="frame_order_pdb_model.html">
-<LINK REL="previous" HREF="frame_order_average_position.html">
-<LINK REL="up" HREF="The_list_of_functions.html">
-<LINK REL="next" HREF="frame_order_pdb_model.html">
-</HEAD>
-
-<BODY >
-
-<DIV CLASS="navigation"><!--Navigation Panel-->
-<A NAME="tex2html17105"
- HREF="frame_order_pdb_model.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Next" ALIGN="BOTTOM" BORDER="0"
ALT="next" SRC="next.png"></A>
-<A NAME="tex2html17099"
- HREF="The_list_of_functions.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Up" ALIGN="BOTTOM" BORDER="0" ALT="up"
SRC="up.png"></A>
-<A NAME="tex2html17093"
- HREF="frame_order_average_position.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Previous" ALIGN="BOTTOM" BORDER="0"
ALT="previous" SRC="prev.png"></A>
-<A NAME="tex2html17101"
- HREF="Contents.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Contents" ALIGN="BOTTOM" BORDER="0"
ALT="contents" SRC="contents.png"></A>
-<A NAME="tex2html17103"
- HREF="Index.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Index" ALIGN="BOTTOM" BORDER="0"
ALT="index" SRC="index.png"></A> <A NAME="tex2html1"
- HREF="http://download.gna.org/relax/manual/relax.pdf";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/pdf_icon_nav.png";
- ALT="pdf_icon_nav.png"></A><A NAME="tex2html2"
- HREF="http://www.nmr-relax.com";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/relax_logo_nav.png";
- ALT="relax_logo_nav.png"></A>
-<BR>
-<B> Next:</B> <A NAME="tex2html17106"
- HREF="frame_order_pdb_model.html">frame_order.pdb_model</A>
-<B> Up:</B> <A NAME="tex2html17100"
- HREF="The_list_of_functions.html">The list of functions</A>
-<B> Previous:</B> <A NAME="tex2html17094"
- HREF="frame_order_average_position.html">frame_order.average_position</A>
- <B> <A NAME="tex2html17102"
- HREF="Contents.html">Contents</A></B>
- <B> <A NAME="tex2html17104"
- HREF="Index.html">Index</A></B>
-<BR>
-<BR></DIV>
-<!--End of Navigation Panel-->
-<!--Table of Child-Links-->
-<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
-
-<UL CLASS="ChildLinks">
-<LI><A NAME="tex2html17107"
-
HREF="frame_order_num_int_pts.html#SECTION081245100000000000000">Synopsis</A>
-<LI><A NAME="tex2html17108"
-
HREF="frame_order_num_int_pts.html#SECTION081245200000000000000">Defaults</A>
-<LI><A NAME="tex2html17109"
- HREF="frame_order_num_int_pts.html#SECTION081245300000000000000">Keyword
arguments</A>
-<LI><A NAME="tex2html17110"
-
HREF="frame_order_num_int_pts.html#SECTION081245400000000000000">Description</A>
-</UL>
-<!--End of Table of Child-Links-->
-<HR>
-
-<H2><A NAME="SECTION081245000000000000000"></A> <A
NAME="uf:_frame_order.num_int_pts"></A>
-<BR>
-frame_order.num_int_pts
-</H2>
-<IMG
- WIDTH="128" HEIGHT="128" ALIGN="BOTTOM" BORDER="0"
- SRC="./frame_order.png"
- ALT="Image frame_order"> <IMG
- WIDTH="128" HEIGHT="128" ALIGN="BOTTOM" BORDER="0"
- SRC="./edit-rename.png"
- ALT="Image edit-rename">
-
-<P>
-
-<H3><A NAME="SECTION081245100000000000000">
-Synopsis</A>
-</H3>
-
-<P>
-Set the number of integration points used in the quasi-random Sobol'
sequence<A NAME="32525"></A> during optimisation.
-
-<P>
-
-<H3><A NAME="SECTION081245200000000000000">
-Defaults</A>
-</H3>
-
-<P>
-<DIV ALIGN="LEFT">
-<SPAN CLASS="textsf"><SPAN
CLASS="textbf">frame_order.num_int_pts</SPAN>(num=200000)</SPAN>
-
-</DIV>
-
-<P>
-
-<H3><A NAME="SECTION081245300000000000000">
-Keyword arguments</A>
-</H3>
-
-<P>
- <SPAN CLASS="textsf">num:</SPAN> The number of integration points to use
in the Sobol' sequence<A NAME="32533"></A> during optimisation.
-
-<P>
-
-<H3><A NAME="SECTION081245400000000000000">
-Description</A>
-</H3>
-
-<P>
-This allows the number of integration points used during the Frame Order
target<A NAME="32535"></A> function optimisation to be changed from the
default. This is used in the quasi-random Sobol' sequence<A
NAME="32536"></A> for the numerical integration.
-
-<P>
-
-<BR>
-<BR><HR>
-<ADDRESS>
-The <a href="http://www.nmr-relax.com";>relax</a> <a
href="http://www.nmr-relax.com/manual/";>user manual</a> (<a
href="http://download.gna.org/relax/manual/relax.pdf";>PDF</a>), created
2015-09-30.
-</ADDRESS>
-</BODY>
-</HTML>
r28043 - in /website/manual: frame_order_average_position.html frame_order_num_int_pts.html![http://www.nmr-relax.com/images/pdf_icon_nav.png"](/images/pdf_icon_nav.png"){kind=link}
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