You will find below answers to many questions frequently asked by the users of Assemble. To display/hide each answer, click on the following icons: 
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- Assemble often asks to choose a "service". Why?
The computer-intensive tasks of Assemble are delegated to RNA algorithms available as WebServices. These WebServices are associated to a given task category: 2D prediction, 3D annotation,...
If, for a given task, several WebServices/RNA algorithms are available, Assemble asks the user to choose its favorite one:
Each WebService is described with the name of the algorithm wrapped and the name of the server hosting it. Right now, Assemble uses the WebServices provided by the EBI server and by our own server (PARADISE server).
- When I open an RNA molecule stored in a FASTA file, Assemble asks me twice to choose a service. Why?
Starting from the sequence of a RNA molecule, Assemble needs to compute two sets of data before displaying the 2D model:- a RNA secondary structure: this will delegate the task to a 2D prediction algorithm (like RNAfold or Contrafold)
- a 2D plot of the computed RNA secondary Structure: this will delegate the task to a 2D plot algorithm (like RNAplot)
- For some PDB files, Assemble is asking me to choose an unmodified residue. Why?
When Assemble finds in a PDB file a residue that is not A, U, G or C, it recognizes it as a modified residue. It substitutes it for its unmodified equivalent by checking an embedded dictionary. If Assemble cannot find any correspondence, it asks the user:
You can extend the dictionary of Assemble by editing the following file located in your home directory (for example .... if you're using Windows):.paradise/version_number/tertiary_data/modified_residues.dat
In this file, each modified nucleotide is listed using the following pattern:modified_residue_symbol unmodified_equivalent
- When I ask Assemble to reorganize the helices, some helices didn't move in the 2D plot I recover. Why?
When Assemble reorganizes automatically the RNA helices, it delegates the task to a 2D plot algorithm. The algorithms used by Assemble cannot manage efficiently intermolecular or pseudoknots helices. If such helices are present in an RNA secondary structure, they're ignored by Assemble if you ask for a reorganization of the helices. - Why has Assemble this "strange" option to transform the intermolecular and pseudoknots helices as a set of tertiary interactions?
Intermolecular and pseudoknots helices are not managed efficiently by 2D plotting algorithms used by Assemble (see previous question for details). If you would like to remove them, you can:- check this option. Since 2D prediction algorithms are not able to produce such helices, this option will only affect a RNA secondary structure computed from a tertiary structure
- remove them yourself by editing the RNA secondary structure
- What is the difference between Assemble and PARADISE?
PARADISE is a middle-layer above which are constructed graphical tools like Assemble or S2S. PARADISE provides:- the implementation of the biological concepts manipulated through the graphical tools (tertiary and secondary structures, structural alignments, atoms, helices, nucleotides,...)
- the implementation of a communication protocol to allow the graphical tools to interact with each other (this aspect will be improved with the next releases) and with external elements (like the RNA Web Services).
- Once Assemble is installed and launched for the first time, I observed two new hidden directories in my home directory. Why?
Assemble creates two hidden directories in your home directory:- .assemble: contains the configuration file of Assemble (config.xml), the plugins directory (plugins) and the data of the embedded structural library (mypdb)
- .paradise: contains all the data necessary for the PARADISE middle layer
- Why is the 3D rendering of Assemble so poor in comparison to other 3D viewers like Chimera, VMD or PyMOL?
Assemble has been designed as a modelling tool. If you need to produce pictures for your 3D model, you can export it in a PDB file and open this file with more adapted 3D tools. But we're working on a improved rendering engine for Assemble. - It seems that Assemble is not able to open some PDB files. Why?
Despite the fact that it exists a clear PDB format guide, many PDB files contains some "variations". Since the PDB file parser of Assemble fits to the official PDB format, these variations can produce an error. If you observe such a behaviour, feel free to contact us for help. - I was not able to start Assemble on a computer not connected to the Internet. Why?
Due to its intrinsic properties, Assemble needs to be launched from a computer connected to the Internet, even if you're not planning to use any WebServices (for example, if you just need to load a 3D model). We're trying to remove this limitation. - Will you improve the automation of the 3D modeling workflow?
Yes. This automation will be at the basis of many new features of the 2.0 version of Assemble. - When I wanted to capture an RNA motif, Assemble asked me to center more my 2D model. Why?
If you have this message when trying to capture an RNA motif:
you should translate and/or zoom your 2D plot to fit your selection into the 2D panel. - The textual format used by Assemble to saves its data is different from the "official" RNAML format. Why?
Well observed!! The "official" RNAML format was a little bit too "verbose" to save huge set of data like solved ribosomal tertiary structures along with their computed secondary structure. Consequently, we have introduced two main modifications:- we have reduced the number of elements
- we have splitted the different kind of data (secondary structures, tertiary structures,...) between several files