getting nuts with aromatic

13 Feb 2010

      Dear all,

I'd like to add an atom at the mass center of each aromatic ring 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. I played a while with bonds properties but I can't see the light (Caroline...).

If there is a way to do so for aromatic rings, how complicated would it be to do the same for any kind of 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@uab.es

----- Missatge original -----
De: chimera-dev-request@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@ncsu.edu>
To: chimera-dev@cgl.ucsf.edu
Subject: [chimera-dev] ribbon for circular molecule
Message-ID: <53249.152.1.53.169.1264654126.squirrel@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@cgl.ucsf.edu>
To: Volodymyr Babin <vbabin@ncsu.edu>
Cc: chimera-dev@cgl.ucsf.edu
Subject: Re: [chimera-dev] ribbon for circular molecule
Message-ID: <4B61DE5A.6050907@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@CA:1.A@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@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@cgl.ucsf.edu>
To: Volodymyr Babin <vbabin@ncsu.edu>
Cc: chimera-dev@cgl.ucsf.edu
Subject: Re: [chimera-dev] ribbon for circular molecule
Message-ID: <4B61E799.3070708@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@CA:1.A@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
------------------------------
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Chimera-dev mailing list
Chimera-dev@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
End of Chimera-dev Digest, Vol 72, Issue 9
******************************************

Jean Didier Pie Marechal

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