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@uab.es www: http://asklipio.qf.uab.es

----- Missatge original ----- De: chimera-dev-request@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@sonic.net To: ladam ladam@smbh.univ-paris13.fr Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] Moving a residue and an VRML object Message-ID: 507F142E.4080906@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@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@cgl.ucsf.edu To: Tom Goddard goddard@sonic.net Cc: chimera-dev@cgl.ucsf.edu, ladam ladam@smbh.univ-paris13.fr Subject: Re: [chimera-dev] Moving a residue and an VRML object Message-ID: 507F2F6F.30800@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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

---

Message: 3 Date: Wed, 17 Oct 2012 15:26:03 -0700 From: Eric Pettersen pett@cgl.ucsf.edu To: ladam ladam@smbh.univ-paris13.fr Cc: chimera-dev BB chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] Moving a residue and an VRML object Message-ID: C66C5891-76C8-4D20-B82E-572E6F919DF2@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