[chimerax-users] scalemol extension not working

[Tom Goddard]

Hi André,

  In ChimeraX if you selected the atoms of your structure then use the Python shell from menu Tools / General / Shell and type in this bit of Python code

from chimerax.atomic import selected_atoms
for a in selected_atoms(session):
    a.coord = 1.5 * a.coord

it will scale all atom positions by a factor of 1.5.  This code could be turned into a simple ChimeraX command if you needed to use it many times.  Here are examples of simple Python code to define ChimeraX commands.

	https://rbvi.github.io/chimerax-recipes/

  I am not sure why the old Chimera script does not work in Chimera 1.16.  We have not developed the old Chimera software for about 6 years so I forget the details of how atom coordinates are retrieved.

	Tom


> On Jan 19, 2023, at 3:13 AM, André Graça via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
>  
> Hi everyone,
>  
> I hope to at least get a reply from Tom, but this may need a bit of troubleshooting (?).
>  
> I looked into a very old post of yours, Tom,  about rescaling an atomic model (see it at the end of my email).
> I put everything in place but I get an  error and I wonder if anything has changed with the PDB format since 2005, or some incompatibility with new chimera versions…
>  
> If there is actually a way of doing the same with ChimeraX, that would be incredible =)
>  
> Cheers!
> André
>  
> Error and forwarded message comes now:
> __________________________________________________
> AttributeError Exception in Tk callback
>   Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x00000000079092C8>> (type: <type 'instancemethod'>)
>   Module: <module 'Midas.midas_ui' from 'C:\Program Files\Chimera 1.16\share\Midas\midas_ui.pyc'> (line: 618)
>   Args: (<Tkinter.Event instance at 0x00000000198D8AC8>,)
>   Event type: KeyPress (type num: 2)
> Traceback (innermost last):
>   File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__
>     return apply(self.func, args)
>   File "C:\Program Files\Chimera 1.16\share\Midas\midas_ui.py", line 628, in processCommand
>     midas_text.makeCommand(cmdText)
>   File "C:\Program Files\Chimera 1.16\share\Midas\midas_text.py", line 69, in makeCommand
>     f(c, args)
>   File "C:\Program Files\Chimera 1.16\share\scalemol\ChimeraExtension.py", line 23, in scale_molecule
>     x, y, z = a.coord().xyz.data()
> AttributeError: '_chimera.Point' object has no attribute 'xyz'
>  
> ================================================
>   Event contents:
>     char: 
>     delta: 0
>     height: ??
>     keycode: 13
>     keysym: Return
>     keysym_num: 65293
>     num: ??
>     serial: 14638
>     state: 8
>     time: 154527203
>     type: 2
>     widget: .121252488L.126915336L.428746824L.428747592L.428747720L
>     width: ??
>     x: 228
>     x_root: 288
>     y: -22
>     y_root: 941
> ______________________________________________________________________
>  
>  
>  
>  
>  
>  
>  
>  
> ------- Start of forwarded message -------
>  
> Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT)
> From: Thomas Goddard <goddard at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>>
>  
> Hi Jinghua,
>  
>   By "virus cage pdb file" I guess you mean you placed atoms at
> icosahedral positions, and want to show them connected up to show some
> icosahedral pattern.
>  
>   I think the easiest approach is to open your old session, run a
> command to change the diameter of the cage, then save a new session.
> Below is some Python code that provides a "scalemol" Chimera command.
> Make a directory chimera/share/scalemol in your Chimera distribution
> and put the code below in file chimera/share/scalemol/ChimeraExtension.py.
> Then start Chimera, open the cage PDB model, use menu entry
> Favorites/Command line, and type a command:
>  
>         scalemol 0 1.5
>  
> to make model number 0 bigger by a factor of 1.5.  If you have more than
> one model open you can see the model numbers using Favorites / Model Panel,
> the model number is shown in the left hand column.
>  
>     Tom
>  
>  
> - ----
> scalemol/ChimeraExtension.py code follows:
>  
>  
> # -----------------------------------------------------------------------------
> #
> def scale_molecule(cmdname, args):
>  
>     from Midas.midas_text import error
>  
>     fields = args.split()
>     try:
>         model_num = int(fields[0])
>         factor = float(fields[1])
>     except:
>         error('Syntax error: scalemol <model-number> <factor>')
>         return
>  
>     import chimera
>     mlist = chimera.openModels.list(id = model_num)
>     if len(mlist) == 0:
>         error('scalemol: No model number %d' % model_num)
>         return
>  
>     for model in mlist:
>         for a in model.atoms:
>             x, y, z = a.coord().xyz.data()
>             c = chimera.Coord()
>             c.x, c.y, c.z = (factor*x, factor*y, factor*z)
>             a.setCoord(c)
>         
> # -----------------------------------------------------------------------------
> #
> import Midas.midas_text
> Midas.midas_text.addCommand('scalemol', scale_molecule)
>  
> ------- End of forwarded message -------
>  
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