<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"
<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 Cα
(marked CA) and SC (marked CB) coordinates are output. The CONECT
records specify the Cα - Cα and Cα - SC virtual bonds. Secondary
<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>
<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>
<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>
<P>
+<!--
<H2><A NAME="SECTION00045000000000000000"></A>
<A NAME="sect:whamoutfiles:histograms"></A>
<BR>
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>
<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>