[Chimera-users] suggested improvements

Dougherty, Matthew T matthewd at bcm.edu
Tue Jul 1 20:01:45 PDT 2014


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

yes

What I am finding with EM viruses approaching atomic resolution, is one researcher will produce the EM reconstruction, another segments the ASU, and another does the PDB.  For me to test it I want to generate the entire PDB capsid using the sym command, so I use the icosahedron surface to match the symmetry on EM density, then apply the symmetry to the ASU.  Having the abbreviations in the menu entries would reduce confusion/accidents.


  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.


It would also provide a gold standard tool to determine EMDB compliance. A button on the volume dialog would be good, an abort during reading spitting out the header would be a useful diagnostic. 


Matthew


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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