[Chimera-users] problem with 17/03 build linux 64

Wed Mar 19 13:11:13 PDT 2008

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 Maréchal wrote:

> From: "Jean-Didier [ISO-8859-1] Maréchal" <jeandidier.marechal at uab.es>
> Sender: chimera-users-bounces at cgl.ucsf.edu
> To: chimera-users at 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 at 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 miÃ©, 19-03-2008 a las 12:00 -0700, chimera-users-request at cgl.ucsf.edu
escribiÃ³:
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> Today's Topics:
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>    1. Re: Principal axis of inertia (Eric Pettersen)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 19 Mar 2008 11:47:51 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Principal axis of inertia
> To: "'Chimera BB'" <chimera-users at cgl.ucsf.edu>
> Message-ID: <DDE1C65B-AD42-48C1-9414-91625662D812 at 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)
> > _______________________________________________
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> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
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> End of Chimera-users Digest, Vol 59, Issue 18
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