That should have been fixed in yesterday's daily build, but another bug prevented the daily build from building, so we rebuilt it today and right now there is a fixed daily build on the website!! Greg Couch On Wed, 19 Mar 2008, Jean-Didier Mar�chal wrote:
From: "Jean-Didier [ISO-8859-1] Mar�chal" <jeandidier.marechal@uab.es> Sender: chimera-users-bounces@cgl.ucsf.edu To: chimera-users@cgl.ucsf.edu Date: Wed, 19 Mar 2008 20:35:44 +0100 Subject: [Chimera-users] problem with 17/03 build linux 64 Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted mechanism) Received-SPF: pass (cgl.ucsf.edu: domain of jeandidier.marechal@uab.es designates 158.109.168.135 as permitted sender)
Hi guys,
thanks a lot for the different answers. I wanted to test Elaine's suggestion and I install the last linux 64 build. When running chimera I have: Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 304, in init from chimera import tkgui File "CHIMERA/share/chimera/tkgui.py", line 80, in <module> File "CHIMERA/share/chimera/printer.py", line 444, in <module> AttributeError: 'module' object has no attribute 'No' Some problem in my installation ? All the best JD El mié, 19-03-2008 a las 12:00 -0700, chimera-users-request@cgl.ucsf.edu escribió:
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Today's Topics:
1. Re: Principal axis of inertia (Eric Pettersen)
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Message: 1 Date: Wed, 19 Mar 2008 11:47:51 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] Principal axis of inertia To: "'Chimera BB'" <chimera-users@cgl.ucsf.edu> Message-ID: <DDE1C65B-AD42-48C1-9414-91625662D812@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed
Just wondering why you weighted by atomic number rather than mass (a.element.mass)?
--Eric
On Mar 19, 2008, at 11:42 AM, Tom Goddard wrote:
Hi JD,
Attached is a script that computes the inertia axes of molecules. Open a molecule, then open the script. It will print the axes in the reply log and show an inertia ellipsoid. It is weighting the atoms by their atomic number, not by the average isotopic mass. Tested in Chimera 1.2498. Should work in older Chimera versions.
Tom
Jean-Didier Mar?chal wrote:
Hi everyone,
I was wondering if there is a method available to calculate the principal axis of inertia of a protein (or a part of a protein) in chimera?
If not what would be the easiest way to move forward?
All the best,
JD
# ---------------------------------------------------------------------- ------- # Compute inertia tensor principle axes for molecule. # def inertia_ellipsoid(m):
atoms = m.atoms n = len(atoms) from _multiscale import get_atom_coordinates xyz = get_atom_coordinates(atoms) anum = [a.element.number for a in atoms] from numpy import array, dot, outer, argsort, linalg wxyz = array(anum).reshape((n,1)) * xyz mass = sum(anum)
c = wxyz.sum(axis = 0) / mass # Center of mass v33 = dot(xyz.transpose(), wxyz) / mass - outer(c,c) eval, evect = linalg.eigh(v33)
# Sort by eigenvalue size. order = argsort(eval) seval = eval[order] sevect = evect[:,order]
return sevect, seval, c
# ---------------------------------------------------------------------- ------- # def ellipsoid_surface(center, axes, lengths, color = (.7,.7,.7,1)):
from Icosahedron import icosahedron_triangulation varray, tarray = icosahedron_triangulation(subdivision_levels = 3, sphere_factor = 1.0) from numpy import dot, multiply es = dot(varray, axes) ee = multiply(es, lengths) ev = dot(ee, axes.transpose()) ev += center
import _surface sm = _surface.SurfaceModel() sm.addPiece(ev, tarray, color) return sm
# ---------------------------------------------------------------------- ------- # def show_ellipsoid(axes, d2, center, model):
from math import sqrt d = [sqrt(e) for e in d2] sm = ellipsoid_surface(center, axes, d) sm.name = 'inertia ellipsoid for %s' % m.name from chimera import openModels as om om.add([sm], sameAs = model)
# ---------------------------------------------------------------------- ------- # def print_axes(axes, d2, m):
from math import sqrt paxes = ['\tv%d = %6.3f %6.3f %6.3f d%d = %6.3f' % (a+1, axes[a][0], axes[a][1], axes[a][2], a+1, sqrt(d2[a])) for a in range(3)] from chimera.replyobj import info info('Inertia axes for %s\n%s\n' % (m.name, '\n'.join(paxes))) from Accelerators.standard_accelerators import show_reply_log show_reply_log()
# ---------------------------------------------------------------------- ------- # from chimera import openModels as om, Molecule mlist = om.list(modelTypes = [Molecule]) for m in mlist: axes, d2, center = inertia_ellipsoid(m) print_axes(axes, d2, m) show_ellipsoid(axes, d2, center, m) _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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