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Vitamine B12. Learning activity (VMD)
Vitamine B12. Learning activity (Maestro)
Branched Alkanes. Learning activity.(VMD)



Vitamin B12. All heavy atoms **Anastasia**
Vitamin B12.
The picture created with VMD.
Selection: all, indexes. One can obtain indexes information via "labels".
Representations: licorice-0.1/0.3; PaperChain: all-flat;licorice-0.2.
Materials: modified MetalPastel, default Opaque, modified Transparent.
Labels added in Gimp.
The picture at the right side is the same representation. But it presents the only active center of the molecule.
Molecule representation made in Maestro find here.
Vitamin B12. Active center

B12 Maestro

B12. Molecular surface colored by elements

Maestro does not provide very powerful representation of a rings - PaperChain. That is why for this molecule it looses much. But it still can provide very understandable molecular surface, that shows from one side opened metal center and its steric properties.


**Volodya**. VMD: lines (all) + licorice(element C N O P) + licorice(element H) + paper(element C N O) + vdw(element P)+vdw(element Co)


Branched alkanes representation

Branched alkanes.
Initially coordinates of several branched alkanes were obtained by creating the molecules with Gaussview (and using the cleaning option for more realistic bond lengths and angles).
The picture was then created with VMD. Each molecule is shown with in a different representation. From left to right (and from top to bottom):
(1) 2-Methylpropane: all, CPK, Opaque.
(2) 2-Methylbutane: all, CPK, Opaque and a second representation with all, VDW, Transparent.
(3) 2,3-Methylbutane: all, Licorice, Opaque.
(4) 2-Methylpentane: all, CPK, Opaque and all, Surf, Opaque, Wireframe.
(5) 2,3-Methylpentane: all, Polyhedra, Opaque.
(6) 2,3,4-Methylpentane: all, Lines, Thickness 4.
As one can fairly easy seen, not all representation can provide the reader with the same information. Structure (1) and (3) are often used, three dimensional distribution of atoms as well as angles can be seen because of a nice light and shadow play. With (6) it is very difficult to get the impression of all three dimensions. (5) seems at the first glance not to give any information, but on a second try one can find all C-atoms in the middle of one tetrahedra, but again angles are quite difficult to evaluate. Overlapping the structure with a wireframe (4) or transparent surface (2) may help to get a better impression of the real size of the molecule and can be also colored according to electronic structure (e.g. charges or hydrophilic and hydrophibic parts), which is often very useful.
In all cases one should not try to put too many information in one picture and let it be as clean and clear as possible.



3AG1 rendered in Molekel

3AG1 rendered in VMD

water surf molekel

the transparent surface is not uniformly transparent