[chimera-dev] sort a list of residues based on the id.position values
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Fri Oct 26 06:49:12 PDT 2012
Hi guys,
how could I sort a list of residues based on their id.position value?
thanks a lot
jd
Dr. Jean-Didier Maréchal
Lecturer
The Computational Biotechnological Chemistry Team
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es
www: http://asklipio.qf.uab.es
----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dijous, Octubre 18, 2012 9:00 pm
Assumpte: Chimera-dev Digest, Vol 102, Issue 5
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> Today's Topics:
>
> 1. Re: Moving a residue and an VRML object (Tom Goddard)
> 2. Re: Moving a residue and an VRML object (Greg Couch)
> 3. Re: Moving a residue and an VRML object (Eric Pettersen)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Wed, 17 Oct 2012 13:25:18 -0700
> From: Tom Goddard <goddard at sonic.net>
> To: ladam <ladam at smbh.univ-paris13.fr>
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] Moving a residue and an VRML object
> Message-ID: <507F142E.4080906 at sonic.net>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> The arrow you drew has no idea that the atoms have moved, so of
> course
> it doesn't move with them. If you just want to rigidly rotate the
> whole
> molecule in Python you can change the matrix that places it in space
>
> mol.openState.xform = xf
>
> instead of changing the coordinates of atoms. Then you could
> rigidly
> move the VRML model in the same way so that the arrow stays in the
> same
> position relative to the molecule.
>
> vrml.openState.xform = xf
>
> If you are not moving the molecule rigidly then you really do need
> to
> move individual atoms and then you will have to delete the old
> arrow and
> make a new arrow if it is intended to have its ends follow certain
> atoms.
> Tom
>
>
> -------- Original Message --------
> Subject: [chimera-dev] Moving a residue and an VRML object
> From: ladam
> To: chimera-dev at cgl.ucsf.edu
> Date: 10/17/12 4:45 AM
> > Hi all,
> > I have a problem associating a vrml object an a molecule :
> > Let's say I have an arrow created using the bild format to which
> I gave
> > 0.0 0.0 0.0 coordinates.
> > This arrow and the molecule translate/rotate together using the
> mouse.> Now if I translate / rotate my molecule using the setcoord
> command on
> > the atoms in a python script, the arrow won't follow up the
> molecule.> I tried the addAssociatedModel command to link the arrow
> and the
> > molecule but still the same result.
> > How can I handle this?
> > Thanks for your attention
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 17 Oct 2012 15:21:35 -0700
> From: Greg Couch <gregc at cgl.ucsf.edu>
> To: Tom Goddard <goddard at sonic.net>
> Cc: chimera-dev at cgl.ucsf.edu, ladam <ladam at smbh.univ-paris13.fr>
> Subject: Re: [chimera-dev] Moving a residue and an VRML object
> Message-ID: <507F2F6F.30800 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Salut,
>
> The other trick is to give the VRML model the same model id and
> submodel
> id as its associated model. Then the openState is identical, so
> there
> would be no need to copy the transformation matrix. Again, this
> only
> works for rigid rotations.
>
> -- Greg
>
> On 10/17/2012 01:25 PM, Tom Goddard wrote:
> > The arrow you drew has no idea that the atoms have moved, so of
> course
> > it doesn't move with them. If you just want to rigidly rotate
> the
> > whole molecule in Python you can change the matrix that places it
> in
> > space
> >
> > mol.openState.xform = xf
> >
> > instead of changing the coordinates of atoms. Then you could
> rigidly
> > move the VRML model in the same way so that the arrow stays in
> the
> > same position relative to the molecule.
> >
> > vrml.openState.xform = xf
> >
> > If you are not moving the molecule rigidly then you really do
> need to
> > move individual atoms and then you will have to delete the old
> arrow
> > and make a new arrow if it is intended to have its ends follow
> certain
> > atoms.
> >
> > Tom
> >
> >
> > -------- Original Message --------
> > Subject: [chimera-dev] Moving a residue and an VRML object
> > From: ladam
> > To: chimera-dev at cgl.ucsf.edu
> > Date: 10/17/12 4:45 AM
> >> Hi all,
> >> I have a problem associating a vrml object an a molecule :
> >> Let's say I have an arrow created using the bild format to which
> I gave
> >> 0.0 0.0 0.0 coordinates.
> >> This arrow and the molecule translate/rotate together using the
> mouse.>> Now if I translate / rotate my molecule using the setcoord
> command on
> >> the atoms in a python script, the arrow won't follow up the
> molecule.>> I tried the addAssociatedModel command to link the
> arrow and the
> >> molecule but still the same result.
> >> How can I handle this?
> >> Thanks for your attention
> >>
> >
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 17 Oct 2012 15:26:03 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> To: ladam <ladam at smbh.univ-paris13.fr>
> Cc: chimera-dev BB <chimera-dev at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] Moving a residue and an VRML object
> Message-ID: <C66C5891-76C8-4D20-B82E-572E6F919DF2 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> On Oct 17, 2012, at 3:21 PM, Greg Couch wrote:
>
> > Salut,
> >
> > The other trick is to give the VRML model the same model id and
> submodel id as its associated model. Then the openState is
> identical, so there would be no need to copy the transformation
> matrix. Again, this only works for rigid rotations.
>
> ...and the simplest way to do this is to supply the "sameAs"
> keyword, with the associated model as the argument, to the
> openModels.add() or openModels.open() call that you use.
>
> --Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
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