text corrections (CA rms, input/output description)

[django_unres.git] / django_simple / todo / templates / outputs.html

diff --git a/django_simple/todo/templates/outputs.html b/django_simple/todo/templates/outputs.html
index 806afc4..1399dda 100644 (file)
--- a/django_simple/todo/templates/outputs.html
+++ b/django_simple/todo/templates/outputs.html
@@ -38,15 +38,15 @@ Contents</A>
 <LI><A NAME="tex2html36"
   HREF="outputs.html#SECTION00041000000000000000">Summary of the files</A>
 <LI><A NAME="tex2html37"
-  HREF="outputs.html#SECTION00042000000000000000">The structure of the main output file (out)</A>
+  HREF="outputs.html#SECTION00042000000000000000">The structure of the main output file</A>
 <LI><A NAME="tex2html38"
   HREF="outputs.html#SECTION00043000000000000000">The thermodynamic quantity and ensemble average (thermal) files</A>
 <LI><A NAME="tex2html39"
   HREF="outputs.html#SECTION00044000000000000000">The conformation summary with classification (stat) files</A>
-<LI><A NAME="tex2html40"
+<!--<LI><A NAME="tex2html40"
   HREF="outputs.html#SECTION00045000000000000000">The histogram files</A>
 <LI><A NAME="tex2html41"
-  HREF="outputs.html#SECTION00046000000000000000">The rmsd-radius of gyration potential of mean force files</A>
+  HREF="outputs.html#SECTION00046000000000000000">The rmsd-radius of gyration potential of mean force files</A> -->
 <LI><A NAME="tex2html42"
   HREF="outputs.html#SECTION00047000000000000000">The PDB files</A>
 <LI><A NAME="tex2html43"
@@ -287,7 +287,7 @@ The Brookhaven Protein Data Bank format (PDB) files
 
 <P>
 These files are written in PDB standard (see. e.g., 
-ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf<FONT COLOR="#0000ff">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</FONT>). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
+<a href="ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</a>). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
 The C&alpha;
  (marked CA) and SC (marked CB) coordinates are output. The CONECT
 records specify the C&alpha; - C&alpha; and C&alpha; - SC virtual bonds. Secondary
@@ -444,6 +444,7 @@ Summary of the files
 <DT></DT>
 <DD>file.cx - the compressed UNRES coordinate file with information to compute the probability of a given conformation at any temperature.
 
+<!--
 <P>
 </DD>
 <DT></DT>
@@ -459,6 +460,7 @@ Summary of the files
 <DT></DT>
 <DD>file.rmsrgy, file_par_yy.rmsrgy, file_slice_xx.rmsrgy or file_par_yy_slice_xx.rmsrgy - the 2D histogram(s) of rmsd from the experimental structure and radius of gyration.
 
+-->
 <P>
 </DD>
 </DL>
@@ -544,7 +546,7 @@ Bits s, c, and h of level 1 are explained in point 2; bits c and h of level 2 pe
 <H2><A NAME="SECTION00042000000000000000"></A>
 <A NAME="sect:whamoutfiles:output:main"></A>
 <BR>
-The structure of the main output file (out)
+The structure of the main output file
 </H2>
 
 <P>
@@ -850,6 +852,7 @@ The octal/quaternary/binary numbers denoting the class for a fragment at level 1
 
 <P>
 
+<!--
 <H2><A NAME="SECTION00045000000000000000"></A>
 <A NAME="sect:whamoutfiles:histograms"></A>
 <BR>
@@ -902,7 +905,7 @@ A line contains the left boundaries of the radius of gyration - rmsd bin (radius
 With SEPARATE_PARSET, the PMFs corresponding to different parameter sets are printed to separate files.
 
 <P>
-
+-->
 <H2><A NAME="SECTION00047000000000000000"></A>
 <A NAME="sect:whamoutfiles:PDB"></A>
 <BR>
@@ -911,7 +914,7 @@ The PDB files
 
 <P>
 The PDB files with names file_[slice_xx_]Tyyy.pdb, where Tyyy specifies a given replica temperature contain the conformations whose probabilities at replica temperature T sum to 0.99, after sorting the conformations 
-by probabilities in descending order. The PDB files follow the standard format; see ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf<FONT COLOR="#0000ff">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</FONT>.
+by probabilities in descending order. The PDB files follow the standard format; see <a href="ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</a>.
 For single-chain proteins, an example is as follows:
 
 <P>