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 =========================================================================== _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users