We hope you’ve had an opportunity to take a look at the revamped website. If you would like to share your thoughts on usability and design or site performance please take a moment to click on the “Give Feedback” button on the website. This will really help us to make the ChemSpider user experience even better.

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5 Responses to “We welcome your Feedback”

  1. Bob Buntrock says:

    I just tried searching Benlysta, a human Genome Sciences/GSK lupus candidate drug (AP 11/13/10; … lupus drug faces scruitiny) in ChemSpider. I got no hits. Hopefully you could dredge up some service that lists at least a structure). — Bob Buntrock, Buntrock Associates, Orono, ME

  2. Bob Buntrock says:

    Re my comment about no hits for Benlysta (which is a registered mark), the Humane Genome Sciences site also gives the synonym belimumab. Again, no hits. — Bob Buntrock, Buntrock Associates, Orono, ME

  3. David says:

    Hi Bob,

    Having quickly researched belimumab, it appears to be a monoclonal antibody-based treatment. ChemSpider is a database of small molecules and is not suited to storing information on large biomolecules (proteins, antibodies etc). As there are good existing databases that cover this area (eg ChEBI) we have specifically chosen not to include large biomolecules in the database.
    I would point out that there may be a few examples of therapeutic treatments comprising of short peptide sequences (<10 AA) in the database if this is of interest to you. I hope that you will continue to find ChemSpider useful in your work.

    Dave

  4. Jim Hart says:

    Why can’t I turn on hydrogen atoms for the larger molecules? Are they automatically not shown? What am I doing wrong? The “Show Hydrogens” checkbox is checked, but they don’t show. Azithromycin shown only 2 inner hydrogens. Do you not show terminal hydrogens? Are they obvious?

  5. David says:

    Hi Jim,

    The ChemSpider interface itself doesn’t have an option to “show hydrogens” – I am therefore guessing that you are using the 3D view option. This is generated from the underlying mol file using Balloon (http://users.abo.fi/mivainio/balloon/index.php) and displayed using the Jmol viewer (http://jmol.sourceforge.net/). It seems that by default only the hydrogen atoms that are explicitly defined in the underlying mol file are displayed in Jmol.

    However, if you wish to see all of the hydrogen atoms there is a way to get Jmol to display them. In the 3D view (Jmol display) right click on the image to display the options menu. Just over half way down the list there is an entry called “Console” – Click on this and a new window will open as a pop-up displaying 2 boxes. Click on the lower box to enter the command: “calculate hydrogens” (without the double quotes) and press Enter.
    This should result in all of the hydrogen atoms in the molecule being explicitly shown.

    You should note that the console only affects the image that it is called from – that is to say if you use the console to change the small image embedded in the page it will not affect the 3D image of the structure in the Zoom box.

    It is also worth bearing in mind that if there are any undefined stereocentres in a structure the process of 3D image generation will still generate a tetrahedral carbon centre (effectively arbitrarily imposing a configuration at that centre). So it is worth checking that you are looking at an entry that has fully defined stereochemistry when generating a 3D model (as an example try viewing the 3D structure in the following record – http://www.chemspider.com/Chemical-Structure.201.html – which actually has no defined stereocentres)

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