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>
 
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 -------