ESPript  3.0

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Q: What do I need to run ESPript?
ESPript is operated as a Web service. It is accessible with any modern Web browser equipped with a PDF reader. To take advantage of the 3D interactive representations, the molecular visualization program PyMOL is required.

  • Supported Web browsers are:

  • Adobe Reader (version 5 or higher) is recommended to view the ESPript result files in PDF format - official website.

  • Free open-source or commercial version of PyMOL can be used (version 0.99rc6 or higher):
  • Binary legacy version (functional with ESPript) can be downloaded here - freely available for Linux, OS X and Windows.
  • Free open-source versions can be downloaded here (beware: source code only).

Q: How can I produce an ESPript figure with multiple secondary structure elements?
The starting point of an ESPript figure is a protein multiple sequence alignment file in Clustal, FASTA, MultAlin, NPS@ or ProDom format. As an example, you can perform such alignment with online servers like EMBL-EBI Clustal Omega or ClustalW2. Then, you need to upload this file in ESPript to produce a basic multiple alignment figure.

If a 3D structure corresponding to a sequence is known (in PDB or DSSP format only), you can add it to the figure. Please take due note that ESPript is not able to predict protein secondary structures : it only uses experimentally determined structures. Finally, as there is no possibility to have PDB or DSSP files containing multiple structures, you need to add one structure file per sequence.

You can follow the ESPript tutorials to get familiar with such process.

Alternately, you can have a look at ENDscript ( which can help you, in certain cases, to produce complex ESPript figures.

Q: When I submit a job, I cannot find the results anywhere. A click on the RESULT button achieves nothing.
ESPript uses a pop-up window to display the results. In certain browser configurations, an advertisement blocking mechanism prevents this pop-up window to appear.
In this case, ESPript displays an alert box telling the user to specifically deactivate this security before submitting a job.

To do so, and depending on the Web browser you are using, please refer to the following instructions:

In all cases, you need to allow the domain
Once this is done, please restart your Web browser and submit a new job to ESPript.

Q: I have uploaded an alignment file and a secondary structure file. I get the following error: " Fatal error: secondary structure elements are certainly misplaced ". What's wrong?
The Secondary structure depiction section refers to the secondary structure elements to be displayed at the top of the sequence block.
By default, ESPript supposes that the secondary structure file corresponds to the first sequence in the alignment. This is not the case for you.

To solve your issue, you can:
  • Manually change the order of the sequence in your alignment file: put the sequence line corresponding to the secondary structure file first.
  • In the Defining groups section of the ESPript form, you can change the order of the sequences. Example: 10 all (means that the sequence order of your alignment is changed in order to represent sequence number 10 first, then all the others).

Notice that you can insert secondary structure elements at the bottom of an alignment. In this goal, switch to ADV mode.
A BOTTOM secondary structures section is now displayed on the form, where you can put a structure file as input. This latter must correspond to the last sequence of your alignment.

Q: I have generated an ESPript figure. What do the colors mean on the multiple sequence alignment?
Please refer to this chapter of the ESPript User Guide.

Q: In my ESPript figure, which secondary structure element the symbol "η" refers to?
The η symbol refers to a 310-helix.
α-helices, 310-helices and π-helices are displayed as medium, small and large squiggles, respectively. β-strands are rendered as arrows, strict β-turns as TT letters and strict α-turns as TTT.

Q: How can I manually add any feature in a figure generated by ESPript?
PostScript or PDF files generated by ESPript can be edited using Adobe Illustrator. If you experience font issues while displaying PostScript or PDF files in Illustrator, please download the following archive containing CourierPS and SymbolPS fonts. Unzip the archive and install the fonts ('how to' for Windows 7 and later - 'how to' for Mac OS X).
You can also generate PNG or TIFF files and use the image editing software of your choice.

Q: Can I download and install ESPript on my computer or my server?
Due to software license constraints, the server version of ESPript can only be run online through the present website.
However, you can download the standalone ESPript 3.x binary [1.8 Mb] (only available for x86-64 Linux OS) and use it at the command-line.

IMPORTANT: as the ESPript binary uses large stack space, you must increase your kernel stack size before executing it.
It can be done with the following command:   ulimit -s unlimited

Q: I have a problem that is not listed here.
Do not hesitate to contact us ( if you require any further information or if you need some help with ESPript.

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ESPript is an SBGrid supported application

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