ELN - Quick Start Guide and FAQ - Collaborative Research Center 1333

ELN Login CRC 1333

Please find more information about the login to the CRC 1333 version of Chemotion on this internal webpage.

Get started

To get started with Chemotion please watch the following video tutorials:

Part 1: Add collections
Part 2: Add reagents
Part 3: Plan a reaction 1
Part 4: Plan a reaction 2
Part 5: Import structures from SDF (e.g. from ChemDraw)
Part 6: Import structures from Excel

Before you add your data, please make sure you run the CRC 1333 installation of Chemotion –> Look for the CRC logo as browser icon!
Thereby, your data will be saved at the University of Stuttgart and you will be able to share data with your colleagues.

To make sure you report your data according to FAIR principles, please always upload two files of your analytical data:

An image file (*.png, *.jpg) to be able to visualize your data in the ELN
The original primary data of your analytical measurements

Preferably use open data formats (e.g. JCAMP-dx) or text based formats (e.g. *.csv, *.txt, *.xlsx). If these are not available please upload the data in the available proprietary data formats (e.g. *.qps for your physisorption data, “BRUKER zipfiles” for NMR data, …).

Questions and Answers from our ELN workshop on October 5, 2020

Using the ELN, I have to take notes twice as we do not have computers available in the labs. What can I do?

Please ask your supervisor to use "Programmpauschalen-Mittel" from the CRC 1333 to purchase Laptops or Tablets to be used for protocolling your experiments digitally in the labs. If this is not successful, please let us know via sfb1333[at]ipoc.uni-stuttgart.de.

How can I access the CRC 1333-ELN from outside the University of Stuttgart?

The CRC 1333-ELN is directly accessible from the IP areas of all our member institutions: University of Stuttgart, MPI-FKF, University of Paderborn and TU Dresden. Thus, all CRC 1333 members can access the ELN from their home institution without using a VPN client. Accessing the ELN from your home you have to login to the VPN client of one of the CRC 1333 institutions.

Is it possible to enlarge images uploaded in PDF or TIF format?

No, PDF and TIF formats are not supported for visual representation. Please upload the files you want to see represented as enlarged images in PNG or JPG format. PDF files will be supported after the next Update (Status: Jan-2021)

Is there a way to visualize and edit my ASCII File in Chemotion?

No, not at the moment. Please use PNG or JPG files to visualize the data in Chemotion and please additionally upload the ASCII file for archiving. In the future, there will be a tool that converts the text-based formats ASCII, csv and excel to JCAMP-DX which will make representation and editing of those files possible.

Can I edit spectra within Chemotion?

Yes, the plugin "ChemSpectra/Spectra Viewer" enables you to view and edit NMR, IR and mass spectra within Chemotion. Additionally, it willl automatically convert your BRUKER-NMR data from the zip-file to an open file format (JCAMP-DX) making your data comply with "FAIR" principles in the process. IR and mass spectra currently have to be uploaded as JCAMP-DX in the CRC 1333 Chemotion-installation.

Drawing similar structures every time again is tedious, is there a way to reuse existing similar structures?

Yes, just use the structure template function within the "Ketcher Chemical Structure Editor". The "single star" button will save your structure as a template. The "four star" button will show you all your template structures to choose from. Additionally you can duplicate and edit existing reagents/ chemicals or import structures from Chemdraw (see: https://www.youtube.com/watch?v=-Tvzy9u-Ke4&feature=emb_logo).

How can I draw and work with very large structures, e.g. polymer structures with >200 repeat units?

Structures of this size can currently not be drawn for technical reasons. Please use the research plan option to protocol experiments with polymers of this size. In 2021 the new "Generic element tool" will be released which will then make it possible to use chemicals in a reaction with "non-standard" features (e.g. polymers with n> 200,materials where no structure can be drawn, ...)

Where should I put the rotary value?

Please put this value into the free-text description field.

Where should I put the conversion? Is there a field for that?

Please put this value into the free-text description field.

The report button is not active - How can I create a report of an experiment?

Please tick the checkbox in the experiment list first. Then the report function works (green-coloured field, paper and pen).

Can I share my experiments with my colleagues?

Yes this is possible via the light blue button. You can choose permission levels and share with individual Chemotion Users or groups. Groups need to be created by the Admin. (Contact)

Can I add the name of a material instead of a formula?

With the current planning tool for chemical reactions this is not possible. Therefore, please use the "research plan" option for planning experiments using materials. In 2021 the new "Generic element tool" will be released which will then make it possible to use chemicals in a reaction with "non-standard" features (e.g. polymers with n> 200; materials, where no structure can be drawn, ...) . The Admin will then be able to implement such new template forms for materials according to your needs.

I am not a synthetic chemist, is it possible for me to fill in a generic work-flow?

Please use the "Research Plan" option to make notes about non-synthetic experiments. There you can already find the option to fill in a table. This table function will be extended by further "Excel-like" functionality. We will let you know as soon as there is anything new.