ESPript operates as a webserver. It can be accessed with any Web browser equipped with a PDF reader. To take advantage of the interactive 3D representations, the molecular visualisation program PyMOL is required.

• Supported Web browsers are:

• Adobe Acrobat Reader 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):

ESPript uses a pop-up window to display the results. In certain browser configurations, an ad-blocking mechanism prevents this pop-up from appearing. In this case, ESPript will display a warning box asking the user to specifically disable this security before submitting a job.

To do this, please follow the instructions below, depending on the web browser you are using:

• Apple Safari.

• Google Chrome.

• Microsoft Edge.

• Mozilla Firefox.

• Opera.

In all cases, you must allow the two domains espript.ibcp.fr  and  endscript.ibcp.fr
Once this is done, please restart your Web browser and submit a new job to ESPript.

The starting point for an ESPript figure is a protein multiple sequence alignment file in Clustal, FASTA, MultAlin, NPS@ or ProDom format. For example, you can obtain such an alignment using online servers such as EMBL-EBI Clustal Omega. You will then need to upload this file into ESPript to generate a simple multiple alignment figure.

If a 3D structure corresponding to a sequence is known (in PDB, CIF 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 or 3D models (e.g. from AlphaFold, RoseTTAFold, etc.). Finally, as there is no way to have PDB, CIF or DSSP files containing multiple structures, you must add one structure file per sequence.

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

Alternatively, you can have a look at ENDscript (https://endscript.ibcp.fr), which can help you, in certain cases, to produce complex ESPript figures.

The Secondary structure depiction section refers to the secondary structure elements to be displayed at the top of the sequence block.
By default, ESPript assumes that the secondary structure file corresponds to the first sequence in the alignment. This is not the case for you.

There are three ways to solve this problem:

• Change the sequence order in your alignment file: place the sequence line corresponding to the secondary structure file first.

or

• Change the order of the sequences in the Defining groups section of the ESPript form. Example: 10 all ⇒ means that the sequence order of your alignment will be changed so that sequence number 10 is displayed first, followed by all the others.

or

• Switch to ADV mode. In the "Special commands and characters" section of the form, enter the following command: X D 10 (and replace 10 by the line number of the alignment corresponding to the sequence for which you wish to display the secondary structure elements).

If the error message persists, check that the sequence of the alignment is identical to that of the structure file.

Note that you can insert secondary structure elements at the bottom of an alignment. To do this, switch to ADV mode.
A BOTTOM secondary structures section will now appear on the form, where you can enter a structure file as input. The latter must correspond to the last sequence of your alignment.

Please refer to this chapter of the ESPript User Guide.

The η symbol indicates a 3₁₀-helix.
α-helices, 3₁₀-helices and π-helices are shown as medium, small and large squiggles, respectively. β-strands are shown as arrows, strict β-turns as letters TT and strict α-turns as TTT.

PDF and PostScript files generated by ESPript can be edited in programs such as Adobe Illustrator or Inkscape.
You can also generate PNG or TIFF files and use the image editing software of your choice.

Due to software licence restrictions, ESPript can only be run online from this website.
However, you can download the standalone ESPript 3.x binary [3.2 Mb] (only available for x86-64 Linux OS) and use it as a command-line.

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

Do not hesitate to contact us (espript@ibcp.fr) if you need any further information or if you need some help with ESPript.