Provides a collection of Java based tools that will help you draw, visualize and analyze different chemical substances and reactions
What's new in Marvin 19.6.0:
- Bugfixes:
- Editing:
- The label of atoms with implicit hydrogens displayed on the top of the atom was misplaced
- The arrow tool did not snip the target atom while mapping reactions.
Marvin is a fully-featured cross-platform set of applications mainly designed for chemical sketching, visualization and data exploration.
Exhaustive chemical drawing and editing toolkit
Sep 17, 2021 Dec 19, 2017 Free, secure and fast Chemistry Software downloads from the largest Open Source applications and software directory. Apple Mac OS Classic (5) BSD/OS (2) HP-UX (2) IBM AIX (4). XDrawChem is an application for chemistry drawing and analysis. Chemix is a free online editor for drawing lab diagrams. Chemical drawing and publishing software for desktop, web and mobile. Affordable and used by thousands of scientists around the world. Free trial available for immediate download. XDrawChem is a free software program for drawing chemical structural formulas, available for Unix and Mac OS. It is distributed under the GNU GPL. In Microsoft Windows this program is called WinDrawChem.
- This free Mac software can be used to obtain high-quality 2D graphs that are generated from the data provided. The data can be modified using the user-defined formulas and it enable fast reading and plotting. Scientists will be able to use this for ASCII data export and import and to plot graphs in many styles.
- An intuitive molecular editor and visualization tool. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.
With Marvin’s help you can quickly and easily sketch molecules, queries and reactions, characterize molecules directly on the canvas, convert between most used chemical file types and visualize beautifully and accurately rendered 2D and 3D structures.
The Marvin package comes with MarvinSketch, MarvinSpace, MarvinView and the web based Marvin JS that you can download from Marvin’s download page.
As follows, MarvinSketch is a state-of-the-art chemical editor that makes it easy for you to draw chemical structures, reactions and queries. MarvinSketch offers a long list of editing features and it is capable to use various structure based calculation plugins for structures on the canvas.
Makes it easy for you to draw and edit chemical structures
Consequently, MarvinSketch allows you to effortlessly draw molecules using the user-definable templates, context-sensitive popup menus and customizable shortcuts.
With MarvinSpace’s help, you can easily visualize small molecules, nucleic acids, crystals and proteins. By using Marvin’s 3D visualization tools you also have the option to visualize various molecular surfaces, molecular orbitals and volumetric data such as hydrophobicity or electrostatic potential.
MarvinView is an advanced chemical viewer that you can use to view single and multiple chemical structures, reactions, queries and non chemical data stored within the file. Thanks to MarvinView, you can easily browse through the comprehensive library of molecules in either grid or spreadsheet view.
Helps you visualize chemical structures and reactions in both 2D and 3D
In addition to helping you generating and publishing reports, MarvinSpace also enables you to perform structure calculations.
Marvin JS is a lightweight chemical editor mainly made to help you generate standard chemical structures and simple queries via the web.
On the whole, Marvin is a powerful tool-set comprising all the necessary tools for basic structure drawing, along with versatile editing features for molecular manipulations.
Filed under
Marvin was reviewed by Sergiu GatlanMarvin 19.6.0
add to watchlistsend us an update- runs on:
- Mac OS X 10.0 or later (PPC & Intel)
- file size:
- 109 MB
- main category:
- Math/Scientific
- developer:
- visit homepage
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This page gives instructions on how to download the software you will need for organic chemistry labs. All of them are either free for everyone to use, or free for students at CU because we have a site license.
VPN
VPN (Virtual Private Network) software allows you to connect to the internet via the campus servers. Many of CU's resources require you to either be on-campus, or use VPN to access them. Instructions for downloading the recommended VPN program (currently Cisco AnyConnect) are given on the OIT website. Make sure that after you install the program, you set it up according to the instructions OIT gives you at the link above! Otherwise it won't work.
ChemDraw and Other Chemical Drawing Programs
ChemDraw is installed on all the computers in the organic chemistry labs and helproom; feel free to use it at any time that the labs are open. ChemDraw is also installed in a large number of computer labs around campus. To find a computer lab that has ChemDraw, you can use the OIT Lab Software Search Page.
CU Boulder has purchased a site license for the current version of ChemDraw, so it is free to all students. To download and install a copy of this program on your own Mac or PC, go to the OIT ChemDraw page. You can download the program for Mac or PC, plus the activation code. There is also an in-depth User Guide available on the OIT page.
There are also several free alternatives to ChemDraw available, such as MarvinSketch and ChemDoodle. These programs are also perfectly acceptable to use for preparing your lab reports, but the organic lab staff might not have much experience using these programs and will not necessarily be able to help you.
Excel and Other Spreadsheet Programs
Excel is part of Microsoft Office Suite, which is available on the computers in the chemistry labs and help room, as well as most of the computers in the computer labs on campus. To find a computer lab that has Excel, you can use the OIT Lab Software Search Page. CU also allows students to download and use Office 365 ProPlus for free. Instructions on how to do so are located on the OIT website.
There are also several free alternatives to Excel available, such as Google Spreadsheets and LibreOffice Calc. These programs are also perfectly acceptable to use for preparing your lab reports, but the organic lab staff might not have much experience using these programs and will not necessarily be able to help you.
MestreNova
MestreNova (or MNova) is installed on all the computers in the organic chemistry labs and helproom; feel free to use it at any time that the labs are open. CU Boulder has purchased a site license for MestreNova, so you may download and install a copy of this program on your own Mac, PC, or Linux machine. Note that you must be able to connect to the campus servers to download the license file, and also to activate it. If you're on-campus, you must connect to the internet via UCB Wireless, not UCB Guest. If you're not on campus, you will need to use VPN as described above. Make sure that you're actually setting up and running VPN according to OIT's instructions! Just downloading the VPN will not do anything.
First, if you have an older version of MestreNova installed, uninstall it.
To download the software, go to the OIT MestreNova page and save the most recent installation package on your computer, along with the license zip file.
Run the MestreNova installer. When you are asked what modules you want to install, uncheck the entire 'MestreNova Plugins' list (every plugin should have a red X next to it), but then select 'NMR Plugin'. This is the only plugin for which we have a license. Your list should look like this:
If you try to install modules for which we don't have a license, you might have to uninstall and then reinstall correctly. Mac Users: You will need to click on 'MestReNova' in the top left corner of the screen (near the apple) and then click 'Preferences' from the drop-down list. From the 'Preferences' pop-up box you can click 'Plug-ins' from the icons at the top of the box and 'ignore' everything except the 'NMR' option.
When you run MestreNova for the first time, you should see the 'Registration Wizard'. (If you don't, select 'Get/Install Licenses...' under the [Help] pulldown.) Click on [Install], and navigate to wherever you saved the license file. Select that license file (if it asks if you want to replace your previous license file, choose 'Yes'). You should see a confirmation message indicating that the license file was installed correctly. Click [OK]. After you have installed all licenses, you will need to restart MNova. Look in the bottom right corner of the window (or check the License Manager under [Help]), and you should see a green checkmark:
If you see the green checkmark, MNova should be ready to use. Mac Users: You may have to go through these steps the first time you run the program. If the 'Registration Wizard' window pops up again and again each time you restart MestreNova, it's because you selected the wrong modules to install. Uninstall the program and start over.
If the program was unable to contact the license server, there will be a red X in the bottom right corner and you will see a popup about being unable to contact the server. In this case, first make sure you have followed all the instructions above (especially the part about being connected to UCB Wireless, not UCB Guest!) Mac Users: You may need to go through a few extra steps to fix this issue. First, go to the Help menu, open the License manager, and delete all the licenses. Then, reinstall them from the zip file containing all the licenses, not the extracted folder.
Now that your copy of MestreNova is activated, it will run for up to 90 days without needing to communicate with the license server again. Every time you use the software when you are connected to the campus network, it will automatically update your license extending your time for another 90 days. Therefore, you can use the software offline, away from the campus network for up to 90 days. After this time, however, you will either need to connect by VPN again, or bring your computer onto campus.
What If You Don't Get Your Spectra?
There are several reasons why you might not receive your spectra, or might not be able to open them. This troubleshooting guide should help you fix any issues.
- If you haven’t received an email with your spectrum: You might have input your email incorrectly, or the NMR server might have been unable to send emails for a while. Check the NMR server to see if your spectrum is there by following all these steps:
- Make sure you're either on-campus using UCB Wireless (not UCB Guest) or on VPN.
- Go to the NMR fileserver page. Your browser might complain about the website's security certificate, but you should be able to select 'Continue to website' or something similar. Depending on your browser, this may be listed under advanced options.
- Sign in using the username 'student' and the password '$NMR300' (not your IdentiKey - this won't work).
- Double-click the NMR Data folder. Once it opens, you should see a window with a menu tree in the left pane and some files in the main pane. If not, you might need to click the 'fullscreen' button in the upper right of the window (it looks like a small grey box).
- Go to OChem_Lab → nmr. Then click 'Filter' in the upper right and type in part of your filename. Folders are named as 'Semester_SectionNumber_Initials_SampleName'. So if it's Spring 2019, you're in section 201, your initials are XYZ, and you named your sample 'Acetylferrocene', then your folder will be named 2019S_201_XYZ_Acetylferrocene).
- Select your folder but don't open it. Instead, go to Action → Download. The folder should download as a zip file. You can now work up the spectrum in MestreNova, assuming it contains a FID file; if not, see below for more help.
- If you haven’t received an email and your folder is not on the server: It hasn't been run in the NMR machine yet. Check to see if any of your classmates have spectra available for this lab yet - if most of them are done, it's possible your sample was skipped for some reason. In this case, visit the NMR room at any time that labs are running so you can resubmit it to the queue.
- If you have your folder but there's no FID file inside it: This happens when the tube is successfully inserted into the machine, but the spectrum never gets collected. Often this is because something is wrong with the sample preparation (label is badly wrapped, too much solid precipitate in tube, solvent too low, or non-deuterated solvent). In this case you will have to visit the NMR room at any time that labs are running so you can fix whatever needs fixing and resubmit it to the queue.
- If you have your folder and there's a FID file inside it, but MestreNova won't open it: First, check the bottom right corner of MestreNova. If there's a red circle, something went wrong with your installation so you'll have to try again. If there's a green circle, your license is set up properly. There are two options for opening spectra: either open the entire zipped folder, or unzip the folder and then open the FID file. To unzip a folder in Windows, right-click and select Extract All.
SciFinder and ACS Literature
SciFinder is the most powerful literature-search tool available for chemists, and will allow you to find any compounds with the same or a similar structure to your compound. Before you can use SciFinder, you will need to request an account. Go to the CU library's website and follow the directions there. Once your account has been created, you can log in by going to SciFinder's home page. You must be on campus or using VPN.
The CU Boulder Libraries have recently made a change to off-campus access for the American Chemical Society (ACS) publications. ACS publications will no longer be accessible using the campus VPN. Instead, users will need to log-in to the Library’s EZProxy. You can also lookup particular journal titles that are available electronically by going to the Libraries homepage and then clicking on the link to E-Journals (underneath that big box that says Find Articles) and search for the journal you need. If you are off-campus you will be asked for your identikey username and password. For more information, including a link to a browser extension that makes it easier for you to access Library resources off-campus, click here.
Chemistry Software Download
Avogadro and GAMESS
Chem Drawing Software Free
Avogadro and GAMESS are free software used for computational chemistry. Avogadro is available for Windows, Mac and Linux; it can be downloaded from the Avogadro website. GAMESS can be downloaded from this website (only accessible from on-campus or via VPN). Once you have installed GAMESS, go to the folder where it is installed and open the README file.