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 -------