Actually, it is possible to use the command line to select portions of a multiscale-models generated volume set: it's just not really efficient. Open your structure and apply the BIOMT with multiscale models. Then select all the surfaces of the multiscale structure. Hide the surface representation and then show a ribbon representation. You might have to wait awhile for this to finish on a large structure. This will generate a new model for each subunit that can be selected manually, via command line, or with the model panel. You can then use the multiscale models panel to make color adjustments, show surfaces etc using selections defined in the command line. However, I can say from experience that learning the Python code is worth the effort in the long run. Jonathan

Hi,

I'm wondering if it is possible to select specific volumes generated via the multiscale model tool via the command line? E.g., for a set of 60 biomt matrices I'm interested in coloring the chains generated with matrices 1-20 in one color, matrices 21-40 in another color, and matrices 41-60 in yet another color. Any suggestions on how to accomplish this would be appreciated.

thanks!

Cathy Lawson

*****************************************************************' Catherine Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology 610 Taylor Road Piscataway, NJ 08854 USA http://roma.rutgers.edu http://rutchem.rutgers.edu/~lawson *****************************************************************

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Message: 2 Date: Mon, 26 Jun 2006 18:18:57 -0700 (PDT) From: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Re: [Chimera-users] selecting multiscale model volumes To: cathy.lawson@rutgers.edu Cc: chimera-users@cgl.ucsf.edu Message-ID: <200606270118.k5R1IvGE1909532@guanine.cgl.ucsf.edu>

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'])