Here is some code to scale a molecule size by a given factor. That is
all atoms have their coordinates multiplied by a factor.
Tom
------- Start of forwarded message -------
Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT)
From: Thomas Goddard <goddard(a)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)
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