[chimera-dev] No glue!
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Sat Feb 13 06:25:44 PST 2010
Dear all,
I'd like to add an atom at the mass center of each aromatic fragment of my ligand (I always want to add an atom don't I?).
I know how to calculate cm, put an atom or point, select aromatic ring BUT I am banging my head against the wall to define one entity of each ring separately.
Would it be a lot more complicate to do so for any cyclic moeity.
Thanks for any help!
best,
JD
Dr. Jean-Didier Maréchal
Lecturer
Computational Biotechnological Chemistry @ Transmet
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
----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dijous, Gener 28, 2010 9:00 pm
Assumpte: Chimera-dev Digest, Vol 72, Issue 9
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> Today's Topics:
>
> 1. ribbon for circular molecule (Volodymyr Babin)
> 2. Re: ribbon for circular molecule (Thomas Goddard)
> 3. Re: ribbon for circular molecule (Thomas Goddard)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Wed, 27 Jan 2010 23:48:46 -0500 (EST)
> From: "Volodymyr Babin" <vbabin at ncsu.edu>
> To: chimera-dev at cgl.ucsf.edu
> Subject: [chimera-dev] ribbon for circular molecule
> Message-ID: <53249.152.1.53.169.1264654126.squirrel at webmail.ncsu.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear Sirs,
>
> I am writing to ask for the chimera sources -- I would like to
> visualize a circular molecule using ribbons. As far as I can tell,
> with the current code ribbons always have ends (cannot be closed)
> because of the following snipped from
>
> libs/_chimera/Chimera.toolkit/Ribbon.implementation
>
> 696 Molecule::updateRibbonData()
> 697 {
> 698 clearRibbonData();
> 699
> 700 //
> 701 // For each residue, find the residues before
> and after. 702
> // Note that only residues with valid guide and plane atoms
> 703
> // may be used as the prev/next residue in a ribbon.
> 704 //
> 705 std::map<Residue *, RibbonResidue> rrMap;
> 706 Residue *prev = NULL;
> ^^^^^^^^^^^^^^^^^^^^^
>
> Could you please allow me to check out the svn version of the
> chimera or get (easily compilable) sources of a recent release.
>
> Thank you,
>
> Volodymyr
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 28 Jan 2010 10:58:34 -0800
> From: Thomas Goddard <goddard at cgl.ucsf.edu>
> To: Volodymyr Babin <vbabin at ncsu.edu>
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] ribbon for circular molecule
> Message-ID: <4B61DE5A.6050907 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Volodymyr,
>
> Chimera is not easy to compile because it requires about 40
> third-party libraries as described on the Chimera source code page
> (link
> is on the Chimera download page).
>
> http://www.cgl.ucsf.edu/chimera/sourcecode.html
>
> Also there is a bit of third-party surface calculation code which
> we are
> not allowed to distribute. All the source code is viewable with
> the web
> interface to the SVN repository. We also have a ticket active for
> allowing public access to check-out the entire Chimera SVN tree
>
> http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641
>
> but that has not been done yet.
>
> If your purpose is to make a figure that doesn't have a gap in
> the
> circular molecule then the following trick might achieve that. You
> could make a new molecule that is not closed and has the two
> starting
> residues duplicated at the end (with increasing residue numbers).
> Then
> when you show the ribbon there will be an overlapping stretch.
> Because
> the overlap will not be perfect you can hide the ribbon for one of
> each
> duplicated residue. If you add a couple duplicate residues the
> ribbon
> should come into exact alignment with itself.
>
> I've added your request for circular ribbons to our feature
> request list.
>
> http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
>
> If you can live with circular cross-section tube a command like
>
> shape tube :1-125.A at CA:1.A at CA radius 1
>
> could do it but it does not close nicely -- different tangent
> vector and
> coloring and selection is not as flexible -- the tube is just a
> surface
> model.
>
> Tom
>
>
> > Dear Sirs,
> >
> > I am writing to ask for the chimera sources -- I would like to
> > visualize a circular molecule using ribbons. As far as I can tell,
> > with the current code ribbons always have ends (cannot be closed)
> > because of the following snipped from
> >
> > libs/_chimera/Chimera.toolkit/Ribbon.implementation
> >
> > 696 Molecule::updateRibbonData()
> > 697 {
> > 698 clearRibbonData();
> > 699
> > 700 //
> > 701 // For each residue, find the residues before
> and after. 702
> > // Note that only residues with valid guide and plane atoms
> 703
> > // may be used as the prev/next residue in a ribbon.
> > 704 //
> > 705 std::map<Residue *, RibbonResidue> rrMap;
> > 706 Residue *prev = NULL;
> > ^^^^^^^^^^^^^^^^^^^^^
> >
> > Could you please allow me to check out the svn version of the
> > chimera or get (easily compilable) sources of a recent release.
> >
> > Thank you,
> >
> > Volodymyr
> >
> >
> >
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 28 Jan 2010 11:38:01 -0800
> From: Thomas Goddard <goddard at cgl.ucsf.edu>
> To: Volodymyr Babin <vbabin at ncsu.edu>
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] ribbon for circular molecule
> Message-ID: <4B61E799.3070708 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Volodymyr,
>
> I will try to get public SVN download of Chimera source working.
> It
> would be great if you learned about programming Chimera. This
> particular part of the code is especially difficult though because
> the
> ribbon class is produced by an antiquated in-house C++ code
> generation
> tool called OTF (Object Technology Framework). I'll add you to the
> notification list for the SVN access ticket.
>
> Tom
>
>
> -------- Original Message --------
> Subject: Re: [chimera-dev] ribbon for circular molecule
> From: Volodymyr Babin
> To: Thomas Goddard
> Date: 1/28/10 11:16 AM
>
> > Hi Thomas,
> >
> > thank you for a very detailed reply.
> >
> >> Also there is a bit of third-party surface calculation code
> which we are
> >> not allowed to distribute.
> >
> > I understand that. I probably was imprecise: it would be nice to be
> > able to compute everything but the non-distributable code.
> >
> >> If your purpose is to make a figure that doesn't have a gap
> in the
> >> circular molecule then the following trick might achieve that. You
> >> could make a new molecule that is not closed and has the two
> starting>> residues duplicated at the end (with increasing residue
> numbers). Then
> >> when you show the ribbon there will be an overlapping stretch.
> Because>> the overlap will not be perfect you can hide the ribbon
> for one of each
> >> duplicated residue. If you add a couple duplicate residues the
> ribbon>> should come into exact alignment with itself.
> >
> > Thank you. I tried this before looking at the sources. I have not
> tried> it with the circular cross-section tube though ... thanks.
> >
> >> I've added your request for circular ribbons to our feature request
> >> list.
> >
> > Thank you. I am not sure this is something of general interest and
> > therefore ruled out this option (feature request) deciding to play
> > with it myself. I am new to chimera and must admit that its
> visualization> capabilities are absolutely outstanding ... which is
> another reason
> > I would prefer to learn it through.
> >
> > Thank you & best regards,
> >
> > Volodymyr
> >
>
>
> -------- Original Message --------
> Subject: Re: [chimera-dev] ribbon for circular molecule
> From: Thomas Goddard
> To: Volodymyr Babin
> Date: 1/28/10 10:58 AM
>
> > Hi Volodymyr,
> >
> > Chimera is not easy to compile because it requires about 40
> > third-party libraries as described on the Chimera source code
> page (link
> > is on the Chimera download page).
> >
> > http://www.cgl.ucsf.edu/chimera/sourcecode.html
> >
> > Also there is a bit of third-party surface calculation code which
> we are
> > not allowed to distribute. All the source code is viewable with
> the web
> > interface to the SVN repository. We also have a ticket active
> for
> > allowing public access to check-out the entire Chimera SVN tree
> >
> > http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641
> >
> > but that has not been done yet.
> >
> > If your purpose is to make a figure that doesn't have a gap in
> the
> > circular molecule then the following trick might achieve that.
> You
> > could make a new molecule that is not closed and has the two
> starting
> > residues duplicated at the end (with increasing residue numbers).
> Then
> > when you show the ribbon there will be an overlapping stretch.
> Because
> > the overlap will not be perfect you can hide the ribbon for one
> of each
> > duplicated residue. If you add a couple duplicate residues the
> ribbon
> > should come into exact alignment with itself.
> >
> > I've added your request for circular ribbons to our feature
> request list.
> >
> > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
> >
> > If you can live with circular cross-section tube a command like
> >
> > shape tube :1-125.A at CA:1.A at CA radius 1
> >
> > could do it but it does not close nicely -- different tangent
> vector and
> > coloring and selection is not as flexible -- the tube is just a
> surface
> > model.
> >
> > Tom
> >
> >
> >> Dear Sirs,
> >>
> >> I am writing to ask for the chimera sources -- I would like to
> >> visualize a circular molecule using ribbons. As far as I can tell,
> >> with the current code ribbons always have ends (cannot be closed)
> >> because of the following snipped from
> >>
> >> libs/_chimera/Chimera.toolkit/Ribbon.implementation
> >>
> >> 696 Molecule::updateRibbonData()
> >> 697 {
> >> 698 clearRibbonData();
> >> 699
> >> 700 //
> >> 701 // For each residue, find the residues before and
> >> after. 702 // Note that only residues with valid guide
> and
> >> plane atoms 703 // may be used as the prev/next
> residue in a
> >> ribbon.
> >> 704 //
> >> 705 std::map<Residue *, RibbonResidue> rrMap;
> >> 706 Residue *prev = NULL;
> >> ^^^^^^^^^^^^^^^^^^^^^
> >>
> >> Could you please allow me to check out the svn version of the
> >> chimera or get (easily compilable) sources of a recent release.
> >>
> >> Thank you,
> >>
> >> Volodymyr
> >>
> >>
> >
>
>
> ------------------------------
>
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
>
>
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