[chimera-dev] ribbon for circular molecule

[Thomas Goddard]

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
>>
>>
>