Catana webapp

From the internet (remote)

PDB ID:Download and import

From your device (local)

Choose files or drag them here

PDBUNFFASTAScreenshot

Select structures to export

Merge to one file on export

File name

Export selected structure(s)

Select structures to export

Transform DNA/RNA strands to oxDNA geometry

Renumber unique IDs

File name

Export selected structure(s)

Select structures to export

File name

Export sequences of selected structure(s)

Screenshot resolution upscale

Transparent background

Trim empty space

Preview screenshotDownload screenshot

Screenshot preview:

AlphaFold

Start new prediction

Sequence

Predict remotelyNote: Each prediction task usually takes several hours to complete.

View submitted predictions

Add prediction ID to listSaved predictions:

NameSequenceIDScore

Show (Reload) analysis

Trajectory structure

Trajectory file

Load trajectory

Playback controls

0/0

New structure from current frameCapture screenshot

DNA geometryDefault sequenceAtom generation

Default Catana DNA geometry. Well-supported by all of Catana features.

Input the default FASTA sequence to be used when creating and modifying coarse-grained DNA strands.
If no sequence is set, a random sequence will be generated.

Sequence

Confirm sequence

Set the maximum number of atoms that can be generated by Catana.
Keep in mind that:
1) PDB does not officially allow more than 99,999 atoms in a single model
2) Generating large number of atoms may take a very long time and/or cause Catana to freeze!Set new limit

DNAPeptide

Input DNA sequence:

Sequence

Create ssDNA Create dsDNA

Input one-letter amino acid sequence:

Sequence

Note: The outcome of this procedure is a crude approximation of the peptide structure.For more accurate approach, use the prediction feature of Catana. Create peptide

Position

X

Y

Z

Orientation

X

Y

Z

Camera near:

Camera far:

Fog near:

Fog far:

Reset camera settings

Background color:

Graphics quality:

Show grid:

Show origin axes:

Debug mode:

Scene Controls

Click with middle mouse button to select an object as the center of rotation.
Hold left mouse button to rotate around the center of rotation.
Hold middle mouse button and move the mouse or use mouse scroll wheel to zoom in and out.
Hold right mouse button to translate/pan the camera along the screen plane.

Components (Right Bar)

Components are independent subsystems (structures, lattices, ...) loaded into Catana. The right bar lists all the components in the Workspace panel, while the Inspector shows details of the selected component. There are following core types of components:

Component representing all-atom structure.

To access tools for the manipulation of all-atom structures, choose the layout "All-atom modelling" in the top bar.

Component representing coarse-grained structure.

To access tools for the manipulation of coarse-grained structures, choose the layout "Coarse-grained modelling" in the top bar.

Component representing DNA origami lattice in honeycomb arrangement
Component representing DNA origami lattice in square arrangement

For each component in the Workspace panel, two additional buttons are shown:

Shows/hides this component
Locks/unclocks this component, i.e., making it (im)possible to move it around

Controls Menu (Left Bar)

Allows for modifications of the structures.Choose a layout in the top bar to see the controls relevant for the kind of modelling you wish to perform.

Coarse-grained structure subsection provides tools for modification and in silico modeling on the coarse-grained level.
All-atom structures subsection provides means for modification of fully atomistic structures.

Gizmo panel (Top Right Bar)

Allows to show/hide gizmos for translation and rotation, and modify their behavior.

Move (translate) component mode.

Drag a component in the 3D view to move it along a camera-aligned plane.
Click on a component in the 3D view to show a translation gizmo at the clicked position.

Rotate component mode.

Drag a component in the 3D view to rotate it around the point where the dragging starts.
Click on a component in the 3D view to show a rotation gizmo at the clicked position.

Importing or Creating New Structure

To import new structure, open Structure -> Import... dialog. You can load a structure from the available databases or upload a local file stored in one of many supported file formats.To create structures from scratch, use the Structure -> Create... dialog allowing to design DNA strands and small peptides.

Exporting the Structure

To export the structure, open Structure -> Export... dialog. Catana currently supports export to PDB, UNF, FASTA, and as a screenshot. Multiple structures/components can be selected for export and then exported as one, allowing for fusing different files.

Structure Prediction

To start a new structure prediction, go to Structure -> Predict... dialog. Here, you can initiate new prediction based on your desired sequence, and check the status of submitted predictions.

Catana (Official website) is an online modeling environment for the creation of recombinant proteins and the functionalization of nucleic acid nanostructures. It was developed as a part of the MARILIA project. If you use Catana in your research, we would appreciate it if you can cite our paper.

This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 952110 (MARILIA).

Internet connection:

AlphaFold service:

Converter service:

Bug reporting service:

Full page link: https://catana.ait.ac.at/manual/

Clustering settings

DBSCAN neighbour radius:

DBSCAN minimum points:

Add new cluster defined by a filter

Rigid body physics settings

Physics time step:

Relaxed spring length:

Spring constant:

Start rigid body simulationContinue rigid body simulation

Make explosion at center of mass

Type

All-atomCoarse-grained

Components

_____________

This feature is currently disabled

Select structures for collision detection
Or press 'Start' to include all structures

Imprecision info

Configurations

Lenience (Å)

Visual parameters

Radius (Å)

Shape

OX

Color

Opacity

Thickness

Show boundaries

Start

Scripting language:

JSPythonJavaScript

Output:Run scriptAdd to loaded scriptsDownload script file

Load & RunShared VariablesLast Session

Load plugin or script(s)

Choose files or drag them here

Loaded plugins

Scripts from this plugin (scope)

Run scriptAttach script to the update call

Existing shared variables

Refresh variables' values

Add shared variable

Name:

Value:

Add new variable

Plugins loaded during the last session

Installation will work only for plugins from the official repository.

Send to developers

Hover over a keyword for a detailed description.

Component:

General

NOTANDORHYDROGENSMALLNUCLEOPHILICHYDROPHOBICAROMATICAMIDACIDICBASICCHARGEDPOLARNONPOLARCYCLICALIPHATICSIDECHAINATTACHEDAPOLARHLIGAND@ (atomlist)_ (atom)[ (startresiduelist)/ (model)% (alternatelocation). (atomname): (chain)^ (inscode)PROTEINNUCLEICRNADNAPOLYMERWATERHELIXSHEETTURNBACKBONESIDECHAINALLHETEROIONSUGARBONDEDRINGAROMATICRINGMETALPOLARHNONESCAFFOLDSTAPLE

Chains

Residues

Models

Atoms

Elements

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