CHIMERA: Generating Biomt matrices from a volume

1. Assuming pdb is object #0 and map is #1.

2. Open the chimera command line (Tools -> General Controls -> Command Line). This should appear as a white box at the bottom of your chimera screen.

3. In the command line box, type the following:

measure symmetry #1

////A description of the inferred symmetry and origin will be displayed at the bottom of the screen...check that this is sensible before proceeding!\\\\

sym #0 group #1

////Creates entire symmetric particle...hopefully!\\\\

4. Save your original monomeric particle. The pdb should contain the new biomt matrices in the header. Remember to save relative to your input volume (#1)!

File-> Save PDB...

 Credit to Max to figuring this out! Tried and tested on icosahedral viruses.

CHIMERAX Colouring 

Credit to Pranav for a lot of this one!

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Cool colour palettes...

https://rdrr.io/cran/RColorBrewer/man/ColorBrewer.html

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#setup the environment
open relion_locres.mrc
open relion_locres_filtered.mrc
volume originIndex 224,224,224
open m135_181002a_boxmap.map
open m135_181002a_wholevirus.map
view
view orient

#color surface of map by radius
vol #1-3 hide
color radial #4 palette 100,red:120,yellow:130,green:150,cyan:165,blue
clip far 125
set silhouettes true

volume #4 sdLevel 3.2 step 1
save surface_overview_sdLvl3.2_radial.png  width 1200 height 1200
supersample 3 transparentBackground true
volume #4 sdLevel 7.1 step 1
save surface_overview_sdLvl7.1_radial.png  width 1200 height 1200
supersample 3 transparentBackground true

#colour surface by local resolution
vol #4 hide
vol #2 show
volume #2 sdLevel 6.0 step 1
colordef locres_blue 0.44,0.123,0.182
colordef locres_lt_blue 0.171,0.217,0.233
colordef locres_yellow 0.255,0.255,0.191
colordef locres_orange 0.253,0.174,0.97
colordef locres_red 0.215,0.25,0.28

#color sample #2 map #1 offset 0 palette
locres_blue:locres_lt_blue:locres_yellow:loces_orange:locres_red range
full
color sample #2 map #1 offset 0 palette "dodger blue:sky
blue:khaki:coral:firebrick" range full
save surface_colored_by_locreso.png  width 1200 height 1200
supersample 3 transparentBackground true

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#Colour volume #1 by model #0.

color zone #1 near #0 distance 8

CHIMERA Mask creation

This is a bit buggy.

Check out the cryosparc 2. page for a better protocol for mask creation for local refinements. This is for crude masking.

shape cylinder radius 50 height 60 caps true center #2:1145 coordinateSystem #4

mask ones #13 fullmap true

vop add #3 onGrid #1

///NOTE!

I have found that bsoft does a better job at creating circular masks.

e.g.

bmask -verbose 7 -create 560,560,560 -radius 0,110 -origin 280,280,280 mask.mrc

Type bmask into the command line on rescomp to get the full list of flags and what they mean.