Update README.md

rnaspider support

README.md

@@ -1,4 +1,4 @@
-# SPQR - SPlit and conQueR for RNA structure prediction
+# SPQR - SPlit and conQueR for RNA structure prediction and refinement
 
 SPQR is a coarse-grained representation and energy function for the prediction of the three-dimensional structure of RNA from the knowledge of its sequence [1].
 
@@ -49,27 +49,16 @@ A simple minimization can be run on a pdb file containing a single-strand of RNA
 This script runs internally several simulations which minimize and remove artifacts in order to provide a suitable structure for simulations.
 The script will create and store the results in the folder refSPQR<PDBFILE>. Optionally, the name can be specified with the `-o <OUTPUTNAME>` option.
 The folder will contain a pdb file in SPQR format (`refSPQR<PDBFILE>.pdb`), an all-atom reconstruction (`at_refSPQR<PDBFILE>.pdb`) and a .mc file (`refSPQR<PDBFILE>.mc`), which can be used for further SPQR simulations with full precision (recommended). The all-atom reconstruction is suitable for MD simulations as well.
-The minimization of energy is a good starting point for evaluating the SPQR energy, which is contained in the `.ene` file in the working directory. In addition, it removes clashes and fixes broken bonds, which might be of help when dealing with structures generated by fragment assembly methods, such as the ones generated by Ernwin [4].
-If the secondary structure elements such as hairpins, stems and internal loops are entangled, these artifacts can also be removed automatically [5]. In this case, the secondary structure must be provided in a fasta file containing three lines : a comment line, the sequence and the secondary structure in Vienna format, without pseudoknots. The option `-t <SECONDARYSTRUCTURE>` takes care of this.
-Other options can be found in the user's guide and the help message displayed with the `-h` flag.
+The minimization of energy is a good starting point for evaluating the SPQR energy, which is contained in the `.ene` file in the working directory. In addition, it removes clashes and fixes broken bonds, which might be of help when dealing with structures generated by fragment assembly methods, such as the ones generated by Ernwin [4,5].
 
-In the example contained in the folder `tutorials/entanglement` we have an atomistic pdb structure with its secondary structure in Vienna format. The original structure is entangled. With a short energy minimization we can remove this artifact. 
-Optimal parameters in the `SPQR_REFINE` file have been determined. Just make sure that the script has
+## Disentanglement
+RNA structures generated by a variety of experimental and computational procedures can present artificial entanglements between their secondary structure elements. RNAspider is a tool which allows to quickly identify, visualize and classify such artifacts [6], with a webserver available at [this link] (https://rnaspider.cs.put.poznan.pl). 
+With an entangled pdb structure, its secondary structure (.ss file) and the output file of RNAspider (in csv format), SPQR is able to remove the topological artifacts by carefully displacing the precise nucleotides in the right direction. Starting from an all-atom pdb structure, one must run
 ```
-CLASH_NMC=2000
-CLASH_NSA=20
-CLASH_TSA=5
-LNKRM_STEPS=20
+python spider2spqr.py -i $SPIDERFILE.csv -o $SPQRLIST.lst -p $PDBFILE.pdb -t $SEC_STRUCT.ss
 ```
-keeping the rest of parameters as they come from the source files. The structure can be refined and disentangled using
-```
-./SPQR_REFINE -i entangled.pdb -t entangled.ss -o result
-```
-The final structures are shown below. A better energy minimization can be performed by increasing the length of the simulation for steering the structure towards its initial conformation, by tuning the parameter `ERMSD_NMC`, or minimizing the final energy with the parameter `ENERG_NMC`.
+An example of an entangled structure, together with the csv and secondary structure, is found in the directory `tutorials/RNAspider` , ready to be disentangled!
 
-<p align="center">
-<img src="https://github.com/srnas/spqr/blob/master/doc/src/ent-disent.png" width="800">
-<p>
 ## Visualization
 SPQR pdb files can be visualized in VMD. In order to load the topology, a tcl script must be loaded from the console by running
 ```