NetLaboratory Data Preparation Tool based on Jmol/JME Demo jmetest3.htm as downloaded from https://sourceforge.net/projects/jmol/ and JSM(olecular)E(ditor) by Peter Ertl and Bruno Bienfait and Jmol version 16.3.53 of 2026-03-20. jmetest3 uses Jmol's native 2D to 3D conversion from JSME without use of the NCI/CADD server.

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Stage 1: Draw your molecule in the JSME(ditor) window (left), using the toolbars and the mouse. This is 2D representation.
Click on Yellow smiling face (upper left corner) and get a smiles string. Keep it for your record.
Alternatively, You may click blue triangles (top right 2-nd row or right-click bottom right) and get prompt 'Copy SMILES'. Here You also see prompts to copy other formats. Try 'MOL' and 'MOL V3000'. Be sure, they do not have hydrogens. These are bad news.
Note: Detailed description of the capabilities of JSME can be found here. It is strongly recommended at least to go through this help page compiled by the author himself.
Stage 2: Press the button.
See what appears in the viewer window (right). In the viewer window (right) click right. A menu falls down. Try to keep mouse closer to the top of the window for the menu is rather long. Just above the bottom row press 'Language'. Yes! It speaks a little Russian. Select the language of your convenience. You may also change 'Style/Стиль' as you wish. With use of mouse turn the molecule around to see that what you got is what you wanted.
Note: https://jsme-editor.github.io/dist/JSME_test.html
Stage 3: Again click right in the viewer window (right). Select 'Show/Показать' (close to bottom). In this submenu select 'Extract MOL data/Извлечь MOL данные' - the bottom line. A "console" window pops up. In it you see some text: the part starting from its 4-th row (that starting with two integers) and ending by 'M END' is the structure of your molecule in 'MOL' format. Enjoy - your hydrogens are there. Keep it for your record.
Note 1: It may well happen that You are not going to start Your molecule from the scratch. In any case for a beginner doing so is not a good idea. So, most probably You already have some data. As at the Stage 1, click blue triangles or right-click the JSME(ditor) window (left). A menu falls down. After all 'Copy' promts You will see 'Paste MOL or SDF or SMILES or JME'. This is the first sensible use of SMILES code you have got previously. Try this and see what happens. If You have saved your MOL file try to feed it here and see what happens.
Note 2: Also in case You have some data on Your computer, You may wish to use them. Click-right in JME(ditor) window (right). A menu falls down. Top line reads 'File/Файл' - press it, submenu appears; top line reads 'Load/Загрузить' - press it, submenu appears; top line reads 'Open olcal file/Открыть локальный файл' press it, yet another menu appers close to the top of the JME(ditor) window. Press 'Browse', it brings You to Your filesystem. Go to Your folder with data files and select one. Press 'load' and see what happens. Quite a few input formats are supported:
*.cif, *.cml, *.mol, *.pdb, *.spartan, *.spt, *.xyz.
Good news: Even for formats natively not supporting bonds, like *.cif and/or *.xyz bonds will be assigned on some general chemical common sence.
Good news: Some distributions e.g. Avogadro and JMol itself contain a variety of data in the abovementioned formats. You may wish to download them or others to Your computer and by playing with them improve Your cheminformatics skills.
Good news: Of course we have the data files coming with the JMol distribution on our server. In order to access them click-right in the JME window. A menu falls down. Click 'Console/Консоль' closer to the bottom. The console window pops up. In its lower part insert the command 'load data/caffeine.mol' and press enter. See what happens. A workaround to access other data. Open the page in a new tab. Right-click on it. A menu falls down. In it select 'View Page Source'. There you find plenty of 'load' commands. You may copy them to the console window and by this access the data stored on our server.
TODO: To provide access to the list of data files stored on NetLaboratory server.
Soso news: In the same source window You will find 'load' commands where arguments are preceded by ':', '=', or '$' characters. These are intended to direct You to various large chamical data bases. Of course, You may wish to use them, but whether they are going to be accessible is out of our control.
Bad news: In whatever files in databases and distributives one may find incorrect or insufficient data. The most common fault are missing hydrogenes. Issue the command 'load jpge/mol/adam.mol' in the console window and see what happens. The simple workaround through SMILES not always works, particularly in complex cases (like adam.mol) when the native convertor fails to produce reasonable 3D structure and puts all atoms in one plane. Somewhat simpler example is provided by 'load jpge/mol/bignou01.mol'. It is a relatively simple coordination compound with a macrocyclic organic ligand, but hydrogens (two per carbon plus one per nitrogen) are missing. Restoring them through SMILES + JSME fails (You may try).
Solution: To cope with this the editing capacity of JSmol itself can be used. In order to invoke it right-click on the JSmol window. A menu falls down. Click 'Shaw', submenu appears; click 'Model kit' (just above the bottom line: 'Extract MOL data/Извлечь MOL данные'); a gray stripe appears along the left side of the JSmol window close to the left upper corner. Click on it. A menu appears. Click top row (one with a spacefill icon; there is no literal notation). Submenu appears; in it check radio button marked by 'H' (hydrogen). Then go through carbon and nitrogen atoms in the window and add hydrogens to them by left-clicking and dragging. Watch that two H's are added to each of carbons and one H to each nitrogen. Here they are. But for sure not in their correct geometry positions. Again click-right on the JSMol window. The same menu appears. Tap bottom row (with three dots). Submenu appears; in it click either 'minimize' or 'fix hydrogenes and minimize'. Both are going to work, but the last somewhat faster. Watch what happens. When finished turn molecule around and see that hydrogens of all ethane-like (C₂) units are in staggered conformation - as it should be. In the same submenu You may tap 'save file' row. A window appears; select a file name of Your choice and press OK. Now You have Your molecule with all hydrogens in reasonable places.
Another bad news is incorrect bond typing. An example is provided by 'load jpge/mol/coronene.mol'. You see that all carbons in the structure are single-bonded to each other. This is definitely wrong.
Solution: Again click-right on the JSMol window. The same menu appears. Tap second row (with a balls-an-stick icon). Submenu appears; in it check radio button marked by 'increase order'. Then go with the cursor through carbon-carbon bonds and by clicking on them make a half of them double (a hint in a frame will appear on the screen). Now You may save the corrected *.mol file on Your computer by whatever preferred method. Click-right on the JSMol window. The same menu appears. Tap bottom row (with three dots). Submenu appears; in it click 'exit modelkit mode'. Now You are done.
Some more useful features: Outside the modelkit mode click right to get the general JSmol menu. Go to 'Style' and then to 'Labels'. Select what suiys You better. Setting 'With Atom number' is recommended since these numbers are the numbers in the ordinals in the atoms' list in the *.mol file and are used in its bonds' section to identify bonds, so they may be useful.
Feel free to play around with different options and wait for further instruction.