Meeting summary:

This meeting covered the basics of working with models. Most of the information can be found in the very highly recommended Quickstart and Materials Visualizer tutorials, but here are a few notable points. There is a pretty big library of structures included within Materials Studio, import these from the file menu. There are also various choices for depicting the atoms and bonds: ball and stick, tetrahedra, etc. Right click on a model window to call up the display style dialog to choose these. Next, we showed how to build a model with the crystal builder, specifying the symmetry, the atom types, positions, occupancy. See below, we dropped some Si and Co atoms into a cubic unit cell.

Question, how can I label things? Can I select and show properties? Can I change charge, occupancy, etc?

To simply determine a property of a given atom or bond, open the properties explorer under the view menu. You will open a table showing all properties of selected atoms and bonds in the model. Colors, labels, and so on can be customized. First select some atoms, either by hand with the arrow tool or using the atom selection dialog under the edit menu. Then play with the label dialog under the view menu. To select multiple fields for labeling, hold the ctrl key when selecting. The example below shows labels of element name, symbol, fractional coordinates (very useful!) charge and formal charge. The labels move with the atoms when the model rotates.

The difference between charge and formal charge should be noted. By default on building a model the charge is zero (neutral) but each atom has a formal charge. In this model, the Si shows up with formal charge 4 and the Co with formal charge 2. It would be good for someone to learn more about how this works in terms of the way the program calculates bond lengths.

Question, can I add arrows to the model, are there magnetic space groups, can I draw orbitals ...

Some info:

1. the Reflex (powder diffraction) package makes no provision for magnetic scattering of neutrons, only nuclear.
2. CASTEP can do spin-polarized DFT calculations, but we didn't buy this.
3. VAMP can display a spin polarized electron density (depiction of orbitals), not sure we bought this
4. to define magnetic structures such as an antiferromagnetic unit cell, "it may be necessary to define a supercell or reduce the symmetry"

So, it looks like magnetic crystallography is not among the Visualizer tools. As for orbitals and arrows, there is no "drawing program" aspect to the Visualizer. If we had bought the quantum mechanics code and wanted to calculate electron density isosurfaces (which is where the orbitals come from), this could be done, either spin polarized or not.

Working with the molecule sketcher: first, please work through the tutorial. Note that when sketching, the program works with a fixed bond length that can be directed in the plane of the screen. Bringing the next atom position closer to the adjacent atom actually brings it up into the third dimension, out of the plane (hold the alt key to send it in the opposite direction behind the plane).

Question, is there a "gauge" to tell me how far up/down it goes?

Can I suggest you can trust your eye. It only goes between zero and ninety degrees, and the bond length is fixed. Also, you can always stop sketching, rotate the structure to lie those bonds into the plane, look at and adjust them. Examples below show a clean and finished OXA (the kind of thing I wanted this program for) and some steps in sloppily sketching an oxygen cube. Step 1, we sketch four atoms in plane (starting with the one on the lower left) and toss another on top. Step 2, I have pressed the left arrow key exactly twice. The arrow keys rotate the structure by 45 degrees (note the xyz axes). But instead of straightening out this bond angle, I just continue to sketch. When you hold the cursor over an atom, this atom becomes the connect point for the next one. If you sketch between two existing atoms, you make a bond between them.

When the cube conneections are finished, we can let the program straighten it out and make symmetrical with the "clean" feature. The "clean" button will make decisions about bond angles and distances for any connected molecule. If we put in a cation and re-clean the structure, bond lengths change depending on the charge. By fooling with the charge and formal charge (between 0 and 1, 2 and 3 respectively) I got changes in O-O bond length from 2.44139 to 2.44177 Å. Maybe we need to learn more about how this works.

Other questions:

Surface diffraction, truncation rods, thermal diffuse scattering?

This fancy synchrotron stuff has to be programmed by us, still. However, there is a software developers' kit. It should not be too hard to marry the Materials Studio model building capabilities to our own analysis code for some of these things.

Twinned models?

Yes! Search the tutorials.

Input / output? Ascii files of simulated diffraction data and model structures? Model sharing between MS and other programs?

Yes, it's dead easy. To make this web page I copied models within Materials Studio, pasted them into Adobe Illustrator, and could output them as gif files in about three seconds. Dropping pictures and tables into any windows software will work. I will give examples on this, next meeting.

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