Hi Cathy,

Unfortunately no Chimera commands allow selecting or coloring multiscale surfaces. The multiscale tool in general is not well integrated with the other Chimera capabilities -- like the Actions Color menu won't color chain surfaces that you select with the mouse. We plan on fixing this in the future but it may take a while (6 months or more).

Everything is possible using Python code, although this can be quite difficult to figure out. It is not documented and the best approach is to ask for examples from us that you can then modify. Below is code to color multiscale surfaces with specific matrix subunits and chain IDs. If you open that file in Chimera (with File / Open..., or with the "open" command) it will do the type of coloring you requested. When you modify the code be careful not to change the indentation since this is important in Python.

We could easily do a little better and add a Chimera command so that you would not have to edit a Python script to specify what residue ranges and colors to use.

I am going on vacation tomorrow until July 18 but can make that command for you when I return. It just requires some additional Python code that Chimera will load at startup.

Tom

---- Python file mmcolor.py follows:

# ---------------------------------------------------------------------------- # Color certain matrix subunits and chains of a multiscale model. # def color_multiscale(rgba, model_num, matrix_nums, chain_ids = None):

import MultiScale d = MultiScale.multiscale_model_dialog(True) for cp in d.chain_pieces(): g = cp.surface_group if g.model().id == model_num: mnum, chain_id = g.oslName.split('.') if chain_ids == None or chain_id in chain_ids: if int(mnum) in matrix_nums: cp.set_color(rgba)

# ---------------------------------------------------------------------------- # red = (1,0,0,1) # Red, green, blue, opacity green = (0,1,0,1) blue = (0,0,1,1) cyan = (0,1,1,1)

color_multiscale(blue, 1, range(1,21)) # Color matrix subunits 1-20 color_multiscale(cyan, 1, range(21,41)) # Color matrix subunits 21-40 color_multiscale(green, 1, range(41,61)) # Color matrix subunits 41-60

# Example coloring subunits 1-20, only chains 'A' and 'B'. #color_multiscale(red, 1, range(1,21), ['A', 'B'])