Author: bugman
Date: Fri Jan 12 04:27:10 2007
New Revision: 2987
URL: http://svn.gna.org/viewcvs/relax?rev=2987&view=rev
Log:
Updated the manual and changed the version number to 1.2.10.
Modified:
tags/1.2.10/docs/latex/docstring.tex
tags/1.2.10/docs/latex/relax_version.tex
Modified: tags/1.2.10/docs/latex/docstring.tex
URL:
http://svn.gna.org/viewcvs/relax/tags/1.2.10/docs/latex/docstring.tex?rev=2987&r1=2986&r2=2987&view=diff
==============================================================================
--- tags/1.2.10/docs/latex/docstring.tex (original)
+++ tags/1.2.10/docs/latex/docstring.tex Fri Jan 12 04:27:10 2007
@@ -1648,7 +1648,7 @@
& \\
More and Thuente line search & \quotecmd{\^{}[Mm][Tt]} or
\quotecmd{\^{}[Mm]ore[ \_][Tt]huente\$} \\
& \\
- No line search & \quotecmd{\^{}[Nn]o [Ll]ine [Ss]earch\$} \\
+ No line search & \quotecmd{\^{}[Nn]one\$} \\
\bottomrule
\end{tabular}
\end{center}
@@ -1662,7 +1662,7 @@
\toprule
Hessian modification & Patterns \\
\midrule
- Unmodified Hessian & \quotecmd{\^{}[Nn]o [Hh]essian [Mm]od} \\
+ Unmodified Hessian & \quotecmd{[Nn]one} \\
& \\
Eigenvalue\index{eigenvalues} modification & \quotecmd{\^{}[Ee]igen} \\
& \\
@@ -1679,6 +1679,9 @@
\end{center}
+ As both the line search algorithm and Hessian modification can be specified
for Newton\index{minimisation techniques!Newton} optimisation, supplying the
option \quotecmd{None} may appear to be ambiguous. In fact, the Hessian
takes precedence over the line search. Hence supplying the option
\quotecmd{None} with the Newton\index{minimisation techniques!Newton}
algorithm selects the unmodified Hessian. Supplying \quotecmd{None} twice
will turn off the Hessian modification and no step length selection (or line
search) will be performed.
+
+
Hessian type, these are used in a few of the trust region methods including
the Dogleg\index{minimisation techniques!dogleg} and Exact\index{minimisation
techniques!exact trust region} trust region algorithms. In these cases, when
the Hessian type is set to Newton,\index{minimisation techniques!Newton} a
Hessian modification can also be supplied as above. The default Hessian type
is Newton,\index{minimisation techniques!Newton} and the default Hessian
modification when Newton\index{minimisation techniques!Newton} is selected is
the GMW algorithm.
@@ -2436,15 +2439,15 @@
& & on the timescale of the motions. This is because these \\
& & single timescale models can, at times, be perfect \\
& & approximations to the more complex two timescale models. \\
- & & Hence if $\tau_e$ is less than 100 ps, $S^2$ is plotted.\index{plot}
Otherwise \\
+ & & Hence if $\tau_e$ is less than 200 ps, $S^2$ is plotted.\index{plot}
Otherwise \\
& & the peptide bond is coloured white. The default colour \\
& & gradient is the same as that for $S^2$. \\
& & \\
Amplitude of & \quotecmd{amp\_slow} & Model independent
display\index{display} of the amplite of slow motions, \\
- slow motions. & & arbitrarily defined as motions slower than 100 ps. For
\\
+ slow motions. & & arbitrarily defined as motions slower than 200 ps. For
\\
& & residues described by model-free models m5 to m8, the \\
- & & order\index{order parameter} parameter $S^2$ is plotted\index{plot}
if $\tau_s$ $>$ 100 ps. For models \\
- & & m1 to m4, $S^2$ is plotted\index{plot} if $\tau_e$ $>$ 100 ps. The
default \\
+ & & order\index{order parameter} parameter $S^2$ is plotted\index{plot}
if $\tau_s$ $>$ 200 ps. For models \\
+ & & m1 to m4, $S^2$ is plotted\index{plot} if $\tau_e$ $>$ 200 ps. The
default \\
& & colour gradient is the same as that for $S^2$. \\
& & \\
$\tau_e$. & \quotecmd{te} & The correlation\index{correlation time} time,
$\tau_e$. The default colour gradient \\
@@ -2459,14 +2462,14 @@
Timescale of & \quotecmd{time\_fast} & Model independent
display\index{display} of the timescale of fast \\
fast motions & & motions. For models m5 to m8, only the parameter
$\tau_f$ is \\
& & plotted.\index{plot} For models m2 and m4, the parameter $\tau_e$
is \\
- & & plotted\index{plot} only if it is less than 100 ps. All other \\
+ & & plotted\index{plot} only if it is less than 200 ps. All other \\
& & residues are assumed to have a correlation\index{correlation time}
time of zero. \\
& & The default colour gradient is the same as that of $\tau_e$. \\
& & \\
Timescale of & \quotecmd{time\_slow} & Model independent
display\index{display} of the timescale of slow \\
slow motions & & motions. For models m5 to m8, only the parameter
$\tau_s$ is \\
& & plotted.\index{plot} For models m2 and m4, the parameter $\tau_e$
is \\
- & & plotted\index{plot} only if it is greater than 100 ps. All other \\
+ & & plotted\index{plot} only if it is greater than 200 ps. All other \\
& & residues are coloured white. The default colour gradient \\
& & is the same as that of $\tau_s$. \\
& & \\
@@ -3991,7 +3994,7 @@
\newpage
- \subsection{pdb.read}
+ \subsection{pdb}
\subsubsection{Synopsis}
@@ -4002,7 +4005,7 @@
\subsubsection{Defaults}
- \textsf{\textbf{pdb.read}(self, run=None, file=None, dir=None, model=None,
load\_seq=1)}
+ \textsf{\textbf{pdb}(self, run=None, file=None, dir=None, model=None,
heteronuc=`N', proton=`H', load\_seq=1)}
\subsubsection{Keyword Arguments}
@@ -4015,6 +4018,10 @@
\keyword{ model:} The PDB\index{PDB} model number.
+ \keyword{ heteronuc:} The name of the heteronucleus as specified in the
PDB\index{PDB} file.
+
+ \keyword{ proton:} The name of the proton as specified in the
PDB\index{PDB} file.
+
\keyword{ load\_seq:} A flag specifying whether the
sequence\index{sequence} should be loaded from the PDB\index{PDB} file.
@@ -4028,86 +4035,25 @@
To load the sequence\index{sequence} from the PDB\index{PDB} file, set the
\quotecmd{load\_seq} flag to 1. If the sequence\index{sequence} has
previously been loaded, then this flag will be ignored.
+ Once the PDB\index{PDB} structures are loaded, unit XH bond vectors will be
calculated. The vectors are calculated using the atomic coordinates of the
atoms specified by the arguments heteronuc and proton. If more than one
model structure is loaded, the unit XH vectors for each model will be
calculated and the final unit XH vector will be taken as the average.
+
+
\subsubsection{Example}
- To load all structures from the PDB\index{PDB} file \quotecmd{test.pdb} in
the directory \quotecmd{\~{}/pdb} for use in the model-free analysis run
\quotecmd{m8}, type:
-
-
- \example{relax> pdb.read(`m8', `test.pdb', `\~{}/pdb', 1)}
-
- \example{relax> pdb.read(run=`m8', file=`test.pdb', dir=`pdb', model=1)}
+ To load all structures from the PDB\index{PDB} file \quotecmd{test.pdb} in
the directory \quotecmd{\~{}/pdb} for use in the model-free analysis run
\quotecmd{m8} where the heteronucleus in the PDB\index{PDB} file is
\quotecmd{N} and the proton is \quotecmd{H}, type:
+
+
+ \example{relax> pdb(`m8', `test.pdb', `\~{}/pdb', 1, `N', `H')}
+
+ \example{relax> pdb(run=`m8', file=`test.pdb', dir=`pdb', model=1,
heteronuc=`N', proton=`H')}
To load the 10$^\mathrm{th}$ model from the file \quotecmd{test.pdb}, use:
- \example{relax> pdb.read(`m1', `test.pdb', model=10)}
-
- \example{relax> pdb.read(run=`m1', file=`test.pdb', model=10)}
-
-
-
- \newpage
-
- \subsection{pdb.vectors}
-
-
- \subsubsection{Synopsis}
-
- Function for calculating/extracting XH vectors from the structure.
-
-
-
- \subsubsection{Defaults}
-
- \textsf{\textbf{pdb.vectors}(self, run=None, heteronuc=`N', proton=`H',
res\_num=None, res\_name=None)}
-
-
- \subsubsection{Keyword arguments}
-
- \keyword{run:} The run to assign the vectors to.
-
- \keyword{ heteronuc:} The heteronucleus name as specified in the
PDB\index{PDB} file.
-
- \keyword{ proton:} The name of the proton as specified in the
PDB\index{PDB} file.
-
- \keyword{ res\_num:} The residue number.
-
- \keyword{ res\_name:} The name of the residue.
-
-
-
-
- \subsubsection{Description}
-
- Once the PDB\index{PDB} structures have been loaded, the unit XH bond
vectors must be calculated for the non-spherical diffusion models. The
vectors are calculated using the atomic coordinates of the atoms specified by
the arguments heteronuc and proton. If more than one model structure is
loaded, the unit XH vectors for each model will be calculated and the final
unit XH vector will be taken as the average.
-
-
-
- \subsubsection{Example}
-
- To calculate the XH vectors of the backbone amide nitrogens where in the
PDB\index{PDB} file the backbone nitrogen is called \quotecmd{N} and the
attached proton is called \quotecmd{H}, assuming the run \quotecmd{test},
type:
-
-
- \example{relax> pdb.vectors(`test')}
-
- \example{relax> pdb.vectors(`test', `N')}
-
- \example{relax> pdb.vectors(`test', `N', `H')}
-
- \example{relax> pdb.vectors(`test', heteronuc=`N', proton=`H')}
-
- If the attached proton is called \quotecmd{HN}, type:
-
-
- \example{relax> pdb.vectors(`test', proton=`HN')}
-
- If you are working with RNA, you can use the residue name identifier to
calculate the vectors for each residue separately. For example:
-
-
- \example{relax> pdb.vectors(`m1', `N1', `H1', res\_name=`G')}
-
- \example{relax> pdb.vectors(`m1', `N3', `H3', res\_name=`U')}
+ \example{relax> pdb(`m1', `test.pdb', model=10)}
+
+ \example{relax> pdb(run=`m1', file=`test.pdb', model=10)}
@@ -4829,7 +4775,7 @@
\subsubsection{Defaults}
- \textsf{\textbf{select.read}(self, run=None, file=None, dir=None,
change\_all=0)}
+ \textsf{\textbf{select.read}(self, run=None, file=None, dir=None,
boolean=`OR', change\_all=0, column=0)}
\subsubsection{Keyword Arguments}
@@ -4840,14 +4786,18 @@
\keyword{ dir:} The directory where the file is located.
- \keyword{ change\_all:} A flag specifying if all other residues should be
changed.
+ \keyword{ boolean:} The boolean operator specifying how residues should be
selected.
+
+ \keyword{ change\_all:} A flag specifying if all other residues should be
changed.
+
+ \keyword{ column:} The column containing the residue numbers (defaulting
to 0, the first column).
\subsubsection{Description}
- The file must contain one residue number per line. The number is taken as
the first column of the file and all other columns are ignored. Empty lines
and lines beginning with a hash are ignored.
+ Empty lines and lines beginning with a hash are ignored.
The \quotecmd{change\_all} flag argument default is zero meaning that all
residues currently either selected or unselected will remain that way.
Setting the argument to 1 will cause all residues not specified in the file
to be unselected.
@@ -4856,13 +4806,42 @@
\subsubsection{Examples}
- To select all residues in the file \quotecmd{isolated\_peaks}, type:
+ To select all residues in the file \quotecmd{isolated\_peaks}, type one of:
\example{relax> select.read(`noe', `isolated\_peaks')}
\example{relax> select.read(run=`noe', file=`isolated\_peaks')}
+ To select the residues in the second column of the
relaxation\index{relaxation} data file \quotecmd{r1.600} while deselecting
all other residues, type one of:
+
+
+ \example{relax> select.read(`test', `r1.600', change\_all=1, column=1)}
+
+ \example{relax> select.read(run=`test', file=`r1.600', change\_all=1,
column=1)}
+
+
+ \subsubsection{Boolean operators}
+
+ The \quotecmd{boolean} keyword argument can be used to change how spin
systems are selected. The allowed values are: \quotecmd{OR}, \quotecmd{NOR},
\quotecmd{AND}, \quotecmd{NAND}, \quotecmd{XOR}, \quotecmd{XNOR}. The
following table details how the selections will occur for the different
boolean operators.
+
+
+ \begin{center}
+ \begin{tabular}{llllllllll}
+ \toprule
+ Spin system & 1 & 2 & 3 & 4 & 5 & 6 & 7 & 8 & 9 \\
+ \midrule
+ Original selection & 0 & 1 & 1 & 1 & 1 & 0 & 1 & 0 & 1 \\
+ & & & & & & & & & \\
+ New selection & 0 & 1 & 1 & 1 & 1 & 1 & 0 & 0 & 0 \\
+ \bottomrule
+ \end{tabular}
+ \end{center}
+
+
+ | OR | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | |
| | | | | | | | | | | NOR | 1 | 0 | 0 |
0 | 0 | 0 | 0 | 1 | 0 | | | | | | | | | |
| | | AND | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | |
| | | | | | | | | | | NAND | 1 | 0 |
0 | 0 | 0 | 1 | 1 | 1 | 1 | | | | | | | | |
| | | | XOR | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | |
| | | | | | | | | | | XNOR | 1 |
1 | 1 | 1 | 1 | 0 | 0 | 1 | 0 |
|\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_|\_\_\_|\_\_\_|\_\_\_|\_\_\_|\_\_\_|\_\_\_|\_\_\_|\_\_\_|\_\_\_|
+
+
\newpage
@@ -4878,7 +4857,7 @@
\subsubsection{Defaults}
- \textsf{\textbf{select.res}(self, run=None, num=None, name=None,
change\_all=0)}
+ \textsf{\textbf{select.res}(self, run=None, num=None, name=None,
boolean=`OR', change\_all=0)}
\subsubsection{Keyword Arguments}
@@ -4888,6 +4867,8 @@
\keyword{ num:} The residue number.
\keyword{ name:} The residue name.
+
+ \keyword{ boolean:} The boolean operator specifying how residues should be
selected.
\keyword{ change\_all:} A flag specifying if all other residues should be
changed.
@@ -5552,7 +5533,7 @@
\subsubsection{Defaults}
- \textsf{\textbf{unselect.read}(self, run=None, file=None, dir=None,
change\_all=0)}
+ \textsf{\textbf{unselect.read}(self, run=None, file=None, dir=None,
change\_all=0, column=0)}
\subsubsection{Keyword Arguments}
@@ -5563,14 +5544,16 @@
\keyword{ dir:} The directory where the file is located.
- \keyword{ change\_all:} A flag specifying if all other residues should be
changed.
+ \keyword{ change\_all:} A flag specifying if all other residues should be
changed.
+
+ \keyword{ column:} The column containing the residue numbers (defaulting
to 0, the first column).
\subsubsection{Description}
- The file must contain one residue number per line. The number is taken as
the first column of the file and all other columns are ignored. Empty lines
and lines beginning with a hash are ignored.
+ Empty lines and lines beginning with a hash are ignored.
The \quotecmd{change\_all} flag argument default is zero meaning that all
residues currently either selected or unselected will remain that way.
Setting the argument to 1 will cause all residues not specified in the file
to be selected.
@@ -5585,6 +5568,13 @@
\example{relax> unselect.read(`noe', `unresolved')}
\example{relax> unselect.read(run=`noe', file=`unresolved')}
+
+ To unselect the residues in the second column of the
relaxation\index{relaxation} data file \quotecmd{r1.600} while selecting all
other residues, type one of:
+
+
+ \example{relax> unselect.read(`test', `r1.600', change\_all=1, column=1)}
+
+ \example{relax> unselect.read(run=`test', file=`r1.600', change\_all=1,
column=1)}
Modified: tags/1.2.10/docs/latex/relax_version.tex
URL:
http://svn.gna.org/viewcvs/relax/tags/1.2.10/docs/latex/relax_version.tex?rev=2987&r1=2986&r2=2987&view=diff
==============================================================================
--- tags/1.2.10/docs/latex/relax_version.tex (original)
+++ tags/1.2.10/docs/latex/relax_version.tex Fri Jan 12 04:27:10 2007
@@ -1,1 +1,1 @@
-Version repository checkout
+Version 1.2.10
r2987 - in /tags/1.2.10/docs/latex: docstring.tex relax_version.tex