doc update

[unres.git] / doc / 3.2.1 / latex / unresman.tex

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}