ChemAxon FAQs

Molweight (structure) refers to the calculated molecular weight of the version structure (including charges, isotopes), whereas the Molweight (structure + salt) refers to the calculated molecular weight of the preparation structure together with the salt or solvate which belongs to the version/lot. Molweight (parent) Molweight (version) and Molweight (lot) are molweights supplied by the user.

In case of exact match, the only option is to Accept the match. If other matches (e.g. 2D) besides the exact are also present, no match options will be available for those.

Yes, the Project based access can be enabled (configurable). In this case, registration and access (to be viewed or to be modified) of compounds will be available only if the logged in user has the specified permission within the given project. For a logged in user, the available projects will be displayed in the field drop-down list. No registration will be possible using newly given Project name(s) as additional data. Otherwise, when Project based access is disabled, Project fields can be freely used as additional data, no filtering is made. Note that regardless of the project settings, all the submissions that lack the Project info will be visible.

You can update your catalog without deleting it (but delete and upload also works). Just click on the dots next to your current collection and select Update collection.

There are no strict requirements related to citing Chemicalize. Please mention that the data were calculated using ChemAxon's Chemicalize platform and also include the date of calculation, as well as a reference in a format that is appropriate in the publication (as a bibliography entry or in footnote), e.g. like this: "Chemicalize was used for [prediction of xyz properties/etc], [month and year of use], https://chemicalize.com/, developed by ChemAxon".

If your current Teaching license has expired and you would like a new Teaching license please proceed to apply by logging into your existing account here: https://academia.chemaxon.com/ If your Academic Research license has expired and you need another - Please make sure to upload/ attach a citation paper where you mention/cite ChemAxon or any of our products to your application by logging into your account: https://academia.chemaxon.com/ *Note that if you apply for a new research license but fail to provide a correctly cited paper you will not be granted a new research license.. until you do so!

Yes. Submissions can be modified (e.g. LnbRef, Molweight, Restriction, CST, structure) and then saved. These will be marked as "Saved submissions" in the Staging and their original structure can be restored later or they can be registered.

No. Version level amendment is not allowed for versions without lots. "Editing the structure is not permitted. Amendment of an empty parent/version is not allowed." message can be seen above the structure editor and the Save button (in the Edit mode) is disabled.

There is a template file added, which is not accessible by Marvin. Navigate to your User's home directory and find the chemaxon folder, in which marvin.mytemplates and marvin.templates.properties files are stored. In these files, you can find some url entries for files used as custom template sets. Check if all files are accessible. A faster, but blunt solution is to create a backup copy of these files somewhere, delete the originals from your chemaxon folder and try to relaunch MarvinSketch.

Yes. Polymers can be registered as single-type structures, but as multi-component compounds as well. In order to register as single structures, you can just simply draw structures then click on the Repeating Group tool on the toolbar, select the atoms you want to be included and set the repeat pattern. For more info click here. Registering as multi-component compounds polymers can be stored with its monomer units, that are created by stripping the "leaving groups" (configurable) from the monomers. More details can be found here. The molecular weight and molecular formula of polymers cannot be calculated. Polymers can be stored with its monomer units, that are created by stripping the "leaving groups" (configurable) from the monomers. More details can be found here.

When Marvin installed with no Java bundled is used on a HiDPI monitor and the version of actually installed Java 9+ you may need to manually make an additional setting on Windows. Without it you may experience weird text handling in text boxes and can expect other glitches too. Marvin installed via installer package having Java 11 bundled has this property already set, so you do not need to do anything in addition. This is true for the Windows and Linux installers alike.

Hardened security measures ("notarization") promised by Apple hit the market in the meantime and we are lagging in following this. We are working on the issue and new version will soon comply with these new measures. In case of Marvin you may still run it using command line. Open Terminal and type: /Applications/MarvinSuite/bin/msketch Open System Preferences/Security & Privacy where you see the app under the Allow apps download from section. Press Open Anyway. Next run from command line may bring up dialogs asking for your permission. Allow them to proceed with it.

We handle all of the uploaded chemical structures as private and confidential information. They are not accessible to any other user or third parties, and we do not distribute or publish them in any way. Our staff is technically capable to access your activity history that includes the uploaded structures (for support purposes), however you have the option to permanently delete your activity history and you can also turn off the activity history function. ChemAxon is a trusted partner of many pharmaceutical companies and research institutions, so security and protection of our clients’ data is essential for us.

The Chemically Significant Text (CST) field is especially for that purpose. There is a switcher option available on the Configuration that controls whether the CST only records should be autoregistered or not. If the records fall to the Staging area with "UnknownCST" status message, they can be registered easily from there (Submission page). If the CST is present in the Chem. Sig. Text dictionary (Administration page), the record will be always autoregistered. CSTs can be used also for the user wants to register the same structure but as different compounds (receiving two different parent IDs in the database). If the structures of two compounds are the same (or empty), but the CSTs are different, then these compounds are considered as 2D matches (not as duplicates).

You should switch off the Perform Quality Checks option on the Submission page. You need to have the corresponding privileges to do so.

The “An error occurred while bootstrapping the application” error means that the application cannot be loaded. You always need to clear the browser cache. If you are using Internet Explorer, Edge, Google Chrome, or Mozilla Firefox you can quickly clear cache with a keyboard shortcut. While in your browser, press Ctrl + Shift + Delete simultaneously on the keyboard to open the appropriate window. Make sure that "Cookies" and "Cached images and files" and items "From the beginning of time" is selected when clearing the browsing data, then restart your browser and try to reload again the Compound Registration web application.

How can you cite us? - We would like you to cite our software using the following pattern: was/were used for , , ChemAxon (https://www.chemaxon.com).

On the count of compounds there is no limitation directly, however the bulk upload is limited in size of the uploaded file to ~ 100 Mbytes/file. It can be modified as follows: Edit the {tomcat_home}/webapps/RegistryCxn/WEB-INF/classes/applicationContext.xml file and edit the tag by increasing the value of maxUploadSize property (after saving the file, you have to restart the server):  

No. Greater than 1 parent multiplicities must be used with salt/solvate info. For registering dimer structures you must draw or import the dimer.

Yes, on the Browse-Edit page, from version or lot level, salts/solvates and/or isotopes can be added to the structure. Then click on the Save button. User that have a privileged role can do this.

The Marvin JS license file is most probably provided in a separate license file than the Compound Registration license file. Using the latest Compound Registration version: using the installer wizard both files can be uploaded and the system will automatically merge the two licenses. No "Valid license cannot be found" message should be received in this case. Using C ompound Registration versions older than 17.06.12: the content of the MarvinJS license should be copied into the same license.cxl file that is used for Compound Registration.

When a new OpenJDK version that has no package installer is needed to be installed do the following (example is given for version 13): Download tarball from here Open a terminal window and there: extract archive to the right place: sudo tar -xvf openjdk-13_linux-x64_bin.tar.gz -C /usr/lib/jvm/ create symbolic link: sudo ln -s /usr/lib/jvm/jdk-13 /usr/lib/jvm/java-1.13.0-openjdk-amd64 add java alternative: sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/java-1.13.0-openjdk-amd64/bin/java 1131 Version 13 should be active now. You can check the active java by issuing java -version. If you would like to switch to an other (previously installed) java just type: sudo update-alternatives --config java With this command you can select java versions from list. Java applications started after will use the new java.

If you are able to login without error to ChemAxon Pass, then the problem is related to your system. Please try the latest version of Chrome, Firefox or Edge and also check that you have not disabled cookies and are not using some browser plugins that are interfering with Chemicalize.

In general, our predictors are continuously improving, so different results compared with previous versions are normal. In the vast majority, the most recent version gives the best and most precise results. However, if you find some regression in the current version, please share some specific examples with us, and we do or best to fix it in the upcoming releases.

In the case when there is no exact match and there is one or more 2D / Tautomer / 2D&Tautomer match(es), the match actions are Accept and Unique.

It you're a student or teacher you can can apply for an Academic Research or Teaching license to access these tools. Please proceed to do so here: https://academia.chemaxon.com/ OR No license needed for: Chemicalize: We have a free website that showcases our calculation and predictor tools. Visit the www.chemicalize.com and that's all. It is powered by ChemAxon calculations. Download Marvin: If you want to have a desktop tool, especially useful if you work on a paper or thesis, then register here: https://accounts.chemaxon.com/register (if you didn't do so yet); and simply download our Marvin tool. This is a chemical drawing tool, and it has a calculations menu item on the top. Without a license, you can use that - only for non-commercial purposes. No worries it will pop up an error message that you do not have a license for calculations, but if you hit the OK button, the calculation will run eventually...

For the submissions in the Staging area, a status message is displayed in the last column. When hovering over the status message a detailed message is also displayed for the given submission. If a submission is opened from the Staging in the Submission page, the short and detailed message is also displayed.

If you have an automatic fix available for this checker, you can select it from the popup list of that checker, and, then it will be applied on the fly when you register your structure (in the case of the Racemate Checker the Convert to Unknown fixer can be a possible option). Prior to registration, you can test the effect of the fix using the Check option. If you do not find any appropriate fix for the checker, you have to modify the structure to pass the failing structure checker, or you can contact a Registrar to fix the submission for you.

On the Registration, Submission or Browse-Edit page you can add the salt or solvate then set the appropriate multiplicity. After setting the salt/solvate multiplicity the parent multiplicity can be also set. Please note, that only positive integer numbers can be set for salt multiplicities and positive numbers with one decimal can be set for solvate multiplicities (the decimal places in case of salts/solvates can be configured).

Yes, use the Register with CN option, which is available on the Registration, Submission pages and Browse pages. Note that on the Browse page the option is available only for the selected parent or version level.

No. In case of salt/solvate and/or isotope additions, which can be performed only from lot or version level, the parent Id (PCN) will be always kept.

The Java Platform was designed to allow applications to run on different hardware stacks and operating systems without changes. Java is available on both in 64 and 32 bit versions, allowing users to get the appropriate version for their system. The MarvinSuite's installer is also available for Microsoft Windows both in 64 and 32-bit versions and the two architectures need to match, mismatched versions won't work. You can download the JAVA version of your choice from here. If the Java and the MarvinSketch versions are the same, please set the PATH system variable following this https://www.java.com/en/download/help/path.xml MarvinSuite is also available as 64-bit Marvin installer with bundled openjdk11 from our download page.

ChemDraw has no plugin support for 64-bit web browsers. ChemDraw, if Active X plugin installed, can work fine in 32-bit Internet Explorer (11) or Firefox (older versions than Firefox 52) browsers. Note that ChemDraw has to be installed locally on your computer.

Yes, different types of multi-component compounds exist, based on the level of accuracy of the composition information: alternate, formulation, and mixture. A multi-component compound is distinct from a structure having multiple fragments within a structure field that has been registered as a single compound (without registering each fragment individually). An alternate is a multi-component compound without quantitative composition information. A formulation is a multi-component compound with exact quantitative composition information. A mixture is a multi-component compound with semi-quantitative composition information. It is possible to register polymers as multi-component compounds. Polymers can be stored with its monomer units, that are created by stripping the "leaving groups" (configurable) from the monomers. More details can be found here.

It is possible to configure the system to hide the version level on all the GUI pages and in all confirmation messages, so from the user perspective, the system behaves like the data would be stored only on 2 hierarchy levels. You can also configure the system to generate registration IDs on the lot (preparation/batch) level (e.g.CXN1234-01), which takes care of the lot counter even if you move a lot from one parent to another (it is regenerated according to the new parent). In addition, you can configure the downstream service to neglect the version level, so your downstream systems do not need to even know about it. And, which is the most important: if later you decide to upgrade your system to a 3-level hierarchy, it can be simply done by a configuration!

Single compounds used as components in multi-component compounds can be amended only on parent level. When amending compounds that are used as components in multi-component compounds, the modified structure will be moved to a new tree (and will receive new PCN, CN, LN), in case there is no match in the DB, while the reference of the multi-component compound will be kept with the original compound.

Java applets are not supported by Chrome and Firefox (since Firefox 52 version). But Marvin applet can be still used with InternetExplorer11. Note that you have to allow Java in the browser and the applet is loading very slowly.

Problem: When you open MarvinSketch, it shows that it opened, there is the MarvinSketch icon in the taskbar, but the application is not on your screen. 1. You can try to switch the resolution to 1600 x 900 or something similar, at least temporarily, to see if that makes the MarvinSketch window visible. 2. If you don't want to change the resolution there is another workaround: - Right-click on MarvinSketch shortcut - Properties - Compatibility tab - Change High DPI Settings - High DPI scaling Override section - Tick the checkbox and select System in the drop-down menu

Yes. Multi-component compounds can be amended from lot or version level. They cannot be amended from parent level.

It is configurable. When registering a lot, a structure and/or CST and a valid source are needed for a registration. Usually valid, unique external Ids (like LnbRef) are also set to be required for the registration, but any other fields can be set.

If you want to reset your password simply visit the https://accounts.chemaxon.com/reset page, enter your e-mail address then check your mailbox for your password reset link.

Yes, Marvin applet and ChemDraw are supported, but for the latter one you need a valid installation of ChemDraw on your computer. More details can be found here.

The DB storing of the Registry contains normal JChem tables, and the direct support of the Cartridge is not needed, because the Registry tabled can be directly joined to other JChem Cartridge tables, if required.

Yes, it is possible to register Markush structures within the system. The registered Markush structures are stored separately, but treated the same way as all the other ones: parents, versions and preparations are created; Markush matches are offered during the registration, etc. There are two major limitations: (1) Markush structures cannot be registered automatically, all of them are forced to be reviewed, (2) Markush structures cannot be used as components in multi-component structures. Searching for Markush structures is possible on the Search page, even against the non-Markush structures (in that case all members of the Markush query will be returned as hits, even if they are only part of a multi-component structure).

Yes, there is a specific Upload option for this purpose. You can load an SDFile and map its fields to the appropriate Compound Registration fields (or use a previously saved mapping template), and you can even reset the system switches and the Structure Checker and Autofixer options on the fly. The original and fixed structures can be previewed before initiating the registration. Please note that currently only Single type compounds can be uploaded.

Yes. From version or lot level single compounds can be amended to multi-component ones. The multi-component compound will receive a new PCN, and the new components, if they were not registered yet as single compounds, will receive new parent Ids, to which the components are linked in the multi-component compound.

Multifragment structures can be registered, and are handled as a single molecule. Fragments representing salts/solvates can be automatically extracted and converted to the proper salt/solvate and multiplicity information during the registration process.

Yes, similarly to the compound upload, salt/solvates can be bulk loaded from the Upload page of the application. Salts and/or solvates can be imported from an SDFile after mapping its fields to the appropriate fields (Name and salt solvate flag).

Since January 2016, Microsoft only send security updates for IE11, as it is not under active deployment and earlier versions are officially deprecated. Therefore we don't plan to support IE as it is in end of life state. We fully support Microsoft Edge (the new default browser of Microsoft), Chrome and Firefox.

In the case when the structure change was performed on the parent level, yes. In other cases, when the change was made on version or lot level, new IDs (PCN, CN, LN) will be given.