[Chimera-users] suggested improvements

Tom Goddard goddard at sonic.net
Tue Jul 1 18:59:36 PDT 2014


Hi Matt,

  Is your first suggestion to add the abbreviations 222,2n5,2n3,… to the menu entries in the Icosahedron Surface dialog?

  I agree having the ability to dump an MRC map header would be handy.  I can probably dump that to the Chimera reply log automatically if the MRC map load fails.  I have to think about how to show it in the reply log if the map opens correctly.  I don’t want to dump it to the reply log every time since it would just be useless info in almost all cases.  Not sure we have a Chimera command that I could sneak this into as an option, maybe the “volume” command.

	Tom


On Jun 30, 2014, at 3:54 PM, Dougherty, Matthew T wrote:

> 1) first suggestion
> 
> on the sym command the following is defined
> 
> icosahedral symmetry I[,orientation] around center
> 
>    Example: i,n25 
> 
> where orientation can be:
> 
>    222 (default) - with two-fold symmetry axes along the X, Y, and Z axes
>    2n5 - with two-fold symmetry along X and 5-fold along Z
>    n25 - with two-fold symmetry along Y and 5-fold along Z
>    2n3 - with two-fold symmetry along X and 3-fold along Z
>    222r - same as 222 except rotated 90° about Z
>    2n5r - same as 2n5 except rotated 180° about Y
>    n25r - same as n25 except rotated 180° about X
>    2n3r - same as 2n3 except rotated 180° about Y 
> 
> 
> 
> In the chimera tool->higher order structure -> the icosahedral structure 
> it defines similar orientations, assume in the same order.
> 
> It would be helpful on the selections to include the sym syntax as part of the icosahedral structure text
> ie {222} xyz 2 fold
>   {2n5} x 2 fold z 5 fold
> 
> 
> 
> 
> 2) second suggestion
> When reading an MRC file I occasionally see situations that make me question whether the file is EMDB complaint. 
> 
> It would be good to have the means to dump the MRC header, even if chimera refuses to read the file in its entirety. 
> 
> 
> 
> 
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine
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