PyRy3D Server Tutorial

Modeling solution conformation of a non-coding RNA molecule using PyRy3D web-server

In this tutorial you can learn how to use PyRy3D to build a simple complex model based on data from SAXS experiment. In particular you will learn how to e.g.

  • Prepare input files for analysis
  • Manipulate simulation parameters
  • Analyse results

[ Go to RNA modeling tutorial ]

How to work with PyRy3D server?

To illustrate the use of PyRy3D one can either use "Load Example" button on a Submit website or download example files of the crystal structure of the yjgF gene product from Escherichia coli (pdb code: 1qu9).

All the pdb files and the electron density map, simulated at 20A resolution can be downloaded as a gzip archive from: default.tar.gz or as individual files from the links below.

Job_title: 1qu9

Sequences file:
Components sequences should be provided as a single Multi-FASTa file. Each sequence should be called by structure chain name.

Structures files:
Structures of complex components should be provided as a single .TAR archive containing .PDB files with components coordinates.

Electron density map file:
Electron density map is required in .CCP4/.MRC format.

File with program's parameters:
To provide values of program's parameters use plain text file.

File with distance restraints:
Experimental restraints should be provided in Filtrest3D format.

Full description of Filtrest3D format can be found here:

You can also automatically generate some parts of the file with the tool provided by Filtrest3D authors here:

Attention: the tool does not support logical operators (AND, OR), and surface access, pointdist, symmetry and relation restraint types.

Here are some examples of the input file:
1. to define distance use "dist" keyword and provide information about interacting atoms and the distance (in Angstroms).

dist (
     (E160-F161) "C" -(304-305) "A" (>=1.5)
     (99-107) "B" - (56-70) "A" (<= 0.5)
     (99-105) "B" - (56-70) "A" (<= 0.5)
     (99-100) "B" - (56-70) "A" (CB-CB>=10.0 weight<-10.0)

2. to define which residues are located on the complex surface use "surface access" keyword and provide information about those regions and their distance from the surface (in Angstroms).

surface_access (
     (163-165) "C" (<=1.0)
     (100-101) "B" (<=3.0)

3. to define distance of a given region from point in 3D space use "pointdist" keyword and provide information about those residues and their distance from the point (X,Y,Z coordinates) in 3D space (in Angstroms).

pointdist (
     (100-101) "B"- (0.0,20.0,0.0) (<=5.5)

4. to define which distances in the complex should be of the same length use "symmetry" keyword and provide information about which regions and which atoms you refer to.

symmetry (
  [   (E163-F163) "C"-(306-307) "A" ()
     (100) "B" -(57-60) "A" (CA-CA)
     (100-105) "B" -(57-60) "A" ()
     (99-108) "B" -(56-70) "A" ()
  ]               )

5. to define relation between two distances (e.g. distance between atom A and B is larger than between A and C) use "relation" keyword and provide information about those regions and their relation (>, <, >=, >=, =).

relation (
     (E163-F163) "C" -(306-307) "A" () < (E16-F17) "C" -(100-105) "B" ()

6. to define logical operators between restraints use "AND" or "OR" keyword

     dist ((99-107) "B" - (16-20) "C" (<= 0.5))
     dist ((99-107) "B" - (56-70) "A" (<= 0.5))

PyRy3D returnes an archive with results:
results.tar.gz that contains models and a .log file with reports from a simulation.