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 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.
If you already have data, use the JSME editor menu and choose Paste MOL or SDF or SMILES or JME. Wikipedia articles on organic molecules have SMILES codes for them. See what happens.
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 JSME author himself.
Press the 2D → 3D button.
Inspect the JSMol viewer window (right) and rotate the molecule.
Use the viewer menu to adjust display style if needed.
With use of mouse turn the molecule around to see that what you got is what you wanted.
In the viewer window (right) click right. A menu falls down. Try to keep mouse cursor 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' as you wish.
You may also change 'Style' as you wish.
Outside model kit mode, open the JSmol menu and go to Style → Labels. 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 Style options.
Right-click in the JSmol window (right), A menu falls
down. Top line reads 'File' - press it, submenu appears; top line reads 'Load' - press it,
submenu appears; top line reads 'Open local file' press it, yet another menu appers close to the
top of the JSMol 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,
and .xyz.
Even for formats without explicit bonds, such as .cif and
.xyz, bonds will often be assigned from
some general chemical common sence.
Some distributions, such as Avogadro and JMol itself, contain many files in the supported formats. You may wish to download them or others to Your computer and by playing with them improve Your cheminformatics skills.
Of course, we have the data files coming with the JMol distribution on our server.
In order to
access them click-right in the JSmol window. A menu falls down. Click 'Console/Консоль' closer to the bottom.
A console window pops up. In its lower part insert the command load data/caffeine.mol and
press enter. See what happens.
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.
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.
TODO: To provide access to the list of data files stored on NetLaboratory server.
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).
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 'Show',
submenu appears; click 'Model kit'
(just above the bottom line: Extract MOL data); 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.
Now you can save the corrected file and continue working with proper geometry - strongly recommended.
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.
Again go to Model kit mode clicking-right on the JSMol window, select increase order, then click the carbon-carbon bonds that need to become double bonds. 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. Save the corrected structure.
Right-click the (JSmol) viewer window and choose Show in the fall-down menu
Select Extract MOL data - the bottom line of the menu. Press it.
The console will appear with MOL data with hydrogens included. Copy them and paste to a file on Your computer.