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@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)
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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
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------------------------------
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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End of Chimera-dev Digest, Vol 72, Issue 9 ******************************************