Re: [Jmol-users] hbonds and unit cells in Jmol 10

[Philip B. <pb...@sa...>]

Following up on this:

Is there a scripting way to choose some bonds for different "fatness" 
than others.  I am thinking of the Ferrocene example and a way to show 
the metal coordination bonding differently than the covalent bonding.

Phil Bays

On Jan 28, 2004, at 11:25 AM, Patrick J. Carroll wrote:

>         As per Miguel's questions about my wanting to use hbonds to 
> draw unit cells: I realized I could do a better job with normal bonds 
> and script commands to draw the unit cell edges thin and I can also 
> have the applet display come up immediately with non-default atom and 
> bond sizes by using script commands like:
>
>                 select all;
>                 cpk on;
>                 cpk 0.40;
>                 wireframe on;
>                 wireframe 0.15;
>                 select oxygen;
>                 cpk 0.1;
>                 wireframe 0.1
>
> Take a look at:
>
>                         http://macxray.chem.upenn.edu/cell457b.html
>
>
>         Of course, the better way to draw unit cells would be the 
> capability to read shelxl .res files (which was introduced into Jmol 
> with version 7). These files have all the necessary information. 
> Unfortunately, Jmol 7 has a bug that reads the cell angles incorrectly 
> (Jmol reports alpha, beta, gamma as beta, gamma, alpha). Jmol 8 has an 
> additional bug in that it represents the cell angles in radians rather 
> than degrees. So the Jmol 7 application will only display a correct 
> unit cell for orthogonal cells (all cell angles 90 degrees). But the 
> Jmol 7 applet does not have the capability of displaying "original 
> atoms only" (as the application can) and so it will not draw any atoms 
> that are outside the boundaries of the cell.
>         So for drawing unit cells right now, I don't need anything 
> added to the hbond functionality, but it would be nice to fix the 
> shelxl.res bugs.
>
>
> Pat
>
>
>
>
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