doc update

diff --git a/doc/3.2.1/latex/clusterman.pdf b/doc/3.2.1/latex/clusterman.pdf
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diff --git a/doc/3.2.1/latex/clusterman.tex b/doc/3.2.1/latex/clusterman.tex
index 65b38af..08755e3 100644 (file)
--- a/doc/3.2.1/latex/clusterman.tex
+++ b/doc/3.2.1/latex/clusterman.tex
@@ -353,6 +353,13 @@ Instead of IOPT=1, MINTREE and instead of IOPT=2 MINVAR can be specified
 
 \item{PUNCH\_DIST} -- if present, the upper-triangle of the distance matrix will be 
     printed to a file.
+
+\item{NSAXS} -- number of distance-distribution bins corresponding to to SAXS
+restraints (to be included in further section of the input).
+
+\item{SCAL\_RAD} -- scaling factor of sidechain radii in calculating Gaussian-smoothed distance distribution.
+
+\item{BOXX, BOXY, BOXZ} - periodic-box dimensions.
 \end{description}
 
 \subsubsection{Energy-term weights and parameter files}
@@ -398,6 +405,8 @@ Instead of IOPT=1, MINTREE and instead of IOPT=2 MINVAR can be specified
 
 \item{SCAL14} (0.4) -- scaling factor of 1,4-interactions
 
+\item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term.
+
 \end{description}
 
 \subsubsection{Molecule information}

diff --git a/doc/3.2.1/latex/installman.pdf b/doc/3.2.1/latex/installman.pdf
index 8e958f0..f4acf48 100644 (file)
Binary files a/doc/3.2.1/latex/installman.pdf and b/doc/3.2.1/latex/installman.pdf differ

diff --git a/doc/3.2.1/latex/installman.tex b/doc/3.2.1/latex/installman.tex
index 9e24906..b4d9a12 100644 (file)
--- a/doc/3.2.1/latex/installman.tex
+++ b/doc/3.2.1/latex/installman.tex
@@ -301,14 +301,26 @@ is also specified for the CSA and MINIM component.
 \section{TECHNICAL SUPPORT CONTACT INFORMATION}
 \label{sect:support}
 
-   Dawid Jagie{\l}a\\
+   Cezary Czaplewski\\
    Faculty of Chemistry, University of Gdansk\\
    ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
-   fax: +48 58 523 5012\\
-   e-mail: \href{mailto:lightnir@gmail.com}{lightnir@gmail.com}\\
+   fax: +48 58 523 5128\\
+   e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{cezary.czaplewski@ug.edu.pl}\\
+
+   Adam K. Sieradzan\\
+   Faculty of Chemistry, University of Gdansk\\
+   ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+   fax: +48 58 523 5128\\
+   e-mail: \href{mailto:adams86@wp.pl}{adams86@wp.pl}\\
+
+   Adam Liwo\\
+   Faculty of Chemistry, University of Gdansk\\
+   ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+   fax: +48 58 523 5124\\
+   e-mail: \href{mailto:adam.liwo@ug.edu.pl}{adam.liwo@ug.edu.pl}\\
 
 \small{
-        Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014\\
+        Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014, updated 12/21/2018\\
 }
 
 \end{document}

diff --git a/doc/3.2.1/latex/unresman.pdf b/doc/3.2.1/latex/unresman.pdf
index c67bc1c..cbcb767 100644 (file)
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diff --git a/doc/3.2.1/latex/unresman.tex b/doc/3.2.1/latex/unresman.tex
index 6ec0dc5..bf3de70 100644 (file)
--- a/doc/3.2.1/latex/unresman.tex
+++ b/doc/3.2.1/latex/unresman.tex
@@ -457,6 +457,32 @@ Revised backbone-virtual-bond-angle potentials to treat the L- and D-amino
 acid residues in the coarse-grained united residue (UNRES) force field.
 {\it J. Chem. Theory Comput.}, {\bf 2014}, 10, 2194-2203.
 
+\bibitem{sieradzan_2015}
+A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski.
+Physics-based potentials for the coupling between backbone- and
+side-chain-local conformational states in the united residue
+(UNRES) force field for protein simulations. 
+{\it J. Chem. Theory Comput.}, {\bf 2015}, 11, 817-831.
+
+\bibitem{krupa_2017}
+P. Krupa, A. Ha"labis, W. "Rmudzi"nska, S. O"ldziej, H.A. Scheraga, A. Liwo.
+Maximum Likelihood Calibration of the UNRES Force Field for
+Simulation of Protein Structure and Dynamics.
+\textit{J. Chem. Inf. Model}. \textbf{2017}, 57, 2364-2377
+
+\bibitem{karczynska_2018}
+A.S. Karczy"nska, M.A. Mozolewska, P. Krupa, A. Gie"ldo"n, A. Liwo, C. Czaplewski.
+Prediction of protein structure with the coarse-grained UNRES
+force field assisted by small X-ray scattering data and
+knowledge-based information.
+\textit{Proteins: Struct. Func. Bioinfo.}, \textbf{2018}, 86 (S1), 228-239. %DOI: 10.1002/prot.25421.
+
+\bibitem{czaplewski_2018}
+C. Czaplewski, A. Karczy"nska, A.K. Sieradzan, A. Liwo.
+UNRES server for physics-based coarse-grained simulations and prediction 
+of protein structure, dynamics and thermodynamics.
+\textit{Nucleic Acids Research}, \textbf{2018}, 46, W304-W309.
+
 \end{thebibliography}
 \endgroup
 
@@ -1112,6 +1138,13 @@ See refs. \cite{liwo_1997_02} and \cite{liwo_1997_03}.
 \item{UNRES\_PBD} -- the starting/reference structure is read from an UNRES-generated
             PDB file.
 
+\item{NSAXS} -- number of distance-distribution bins corresponding to to SAXS
+restraints (to be included in further section of the input).
+
+\item{SCAL\_RAD} -- scaling factor of sidechain radii in calculating Gaussian-smoothed distance distribution.
+
+\item{BOXX, BOXY, BOXZ} - periodic-box dimensions.
+
 \end{description}
 
 Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
@@ -1663,7 +1696,7 @@ single run but only temperature exchange.
 
 \end{description}
 
-\subsubsection{Energy-term weights}
+\subsubsection{Energy-term and restraint weights}
 \label{sect:input:main:weights}
 
 (Data list format; subroutine MOLREAD.)
@@ -1712,6 +1745,12 @@ segment, 6rd order contributions).
 \item{WTOR=number} (real) (1.0d0) --
 weight of the torsional term, $U_{tor}$.
 
+\item{WTORD=number} (real) (1.0d0) --
+weight of the double-torsional term, $U_{tord}$.
+
+\item{WSCCOR=number} (real) (1.0d0) --
+weight of the backbone-sidechain-torsional term, $U_{sccor}$.
+
 \item{WANG=number} (real) (1.0d0) --
 weight of the virtual-bond angle bending term, $U_b$.
 
@@ -1734,6 +1773,8 @@ and higher-order correlations.
 \item{DELT\_CORR} (0.5) - thickness of the distance range in which the energy is
 decreased to zero.
 
+\item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term.
+
 \end{description}
 
 The defaults are NOT the recommended values. No ``working'' default values 
@@ -2106,6 +2147,26 @@ ALPHA(i) and OMEG(i) correspond to the side chain attached to CA(i). THETA(i)
 is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
 CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle $\gamma$.
 
+
+\subsubsection{Distance-distribution (SAXS-restraint) data}
+
+This section contains the probability distribution ($P(r)$) from SAXS
+measurements to be used as restraints through introduction of a maximum-likelihood term. 
+Each entry is in a separate like and the number of entries must equal to 
+NSAXS specified in the first data record. Each line contains the position
+of the left side of the distance bin and probability-distribution value, for
+example:
+
+\begin{verbatim}
+0.7100E-00 0.2036E-03
+0.1420E+01 0.4221E-03
+\end{verbatim}
+
+The distance-distribution values do not need to be input in normalized form.
+Normalization is carried out automatically. It should be noted that neither 
+probabilities nor distances can be zero; otherwise the calculations will crash.
+Therefore, entries with zeros must be eliminated from the data.
+
 \subsubsection{Internal coordinates of the initial conformation}
 \label{sect:input:main:intcoord}
 

diff --git a/doc/3.2.1/latex/whamman.pdf b/doc/3.2.1/latex/whamman.pdf
index 9f42835..e2b4252 100644 (file)
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diff --git a/doc/3.2.1/latex/whamman.tex b/doc/3.2.1/latex/whamman.tex
index 3d7670a..1816fdb 100644 (file)
--- a/doc/3.2.1/latex/whamman.tex
+++ b/doc/3.2.1/latex/whamman.tex
@@ -264,6 +264,12 @@ ref \cite{oldziej_2004}.
 
 \item{RESCALE} (1) -- Choice of the type of temperature dependence of the force field.
 
+\item{NSAXS} -- number of distance-distribution bins corresponding to to SAXS
+
+\item{SCAL\_RAD} -- scaling factor of sidechain radii in calculating Gaussian-smoothed distance distribution.
+
+\item{BOXX, BOXY, BOXZ} - periodic-box dimensions.
+
 \begin{description}
 
 \item{$>0$} -- no temperature dependence.
@@ -388,6 +394,7 @@ All items described in this section are input in keyword-based mode.
 \item{WSCCOR} (1.0) -- sequence-specific virtual-bond-torsional energy.
 \item{WDIHC} (0.0) -- dihedral-angle-restraint energy.
 \item{WHPB} (1.0) -- distance-restraint energy.
+\item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term.
 
 \end{description}