F.A.Q. - ENDscript 2

F.A.Q.

F.A.Q.
Q: What do I need to run ENDscript? ENDscript 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: Apple Safari - official website. Google Chrome - official website. Microsoft Edge - official website. Mozilla Firefox - official website. Opera - official website. Adobe Reader (version 5 or higher) is recommended to view the ENDscript 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 ENDscript) can be downloaded here - freely available for Linux, OS X and Windows. Free open-source versions can be downloaded here (beware: source code only). Latest commercial version can be ordered here. Q: When I submit a job, I cannot find the results anywhere. A click on the RESULT button achieves nothing. ENDscript 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, ENDscript 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: Apple Safari. Google Chrome. Microsoft Edge. Mozilla Firefox. Opera. In all cases, you need to allow the two domains `endscript.ibcp.fr` and `espript.ibcp.fr` Once this is done, please restart your Web browser and submit a new job to ENDscript. Q: I have generated an ENDscript flat figure. What do the colors mean on the multiple sequence alignment? Please refer to this chapter of the ESPript User Guide. Q: In my ENDscript flat 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 flat figure generated by ENDscript? PostScript or PDF files generated by ENDscript 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 ENDscript on my computer or my server? Due to software license constraints, ENDscript can only be run online through the present website. Q: I have a problem that is not listed here. Do not hesitate to contact us (espript@ibcp.fr) if you require any further information or if you need some help with ENDscript.

Q: What do I need to run ENDscript?

ENDscript 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:

Apple Safari - official website.

Google Chrome - official website.

Microsoft Edge - official website.

Mozilla Firefox - official website.

Opera - official website.

Adobe Reader (version 5 or higher) is recommended to view the ENDscript 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 ENDscript) can be downloaded here - freely available for Linux, OS X and Windows.

Free open-source versions can be downloaded here (beware: source code only).

Latest commercial version can be ordered here.

Q: When I submit a job, I cannot find the results anywhere. A click on the RESULT button achieves nothing.

ENDscript 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, ENDscript 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:

Apple Safari.

Google Chrome.

Microsoft Edge.

Mozilla Firefox.

Opera.

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

Q: I have generated an ENDscript flat figure. What do the colors mean on the multiple sequence alignment?

Please refer to this chapter of the ESPript User Guide.

Q: In my ENDscript flat 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 flat figure generated by ENDscript?

PostScript or PDF files generated by ENDscript 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 ENDscript on my computer or my server?

Due to software license constraints, ENDscript can only be run online through the present website.

Q: I have a problem that is not listed here.

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

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