Re: [Jmol-developers] JMOL for Simple Gene Modelling

[Robert H. <ha...@st...>]

yes, that should work like a charm. Have fun with this!


On Mon, Apr 6, 2009 at 12:02 PM, Jairav Desai <
jairavdesai2008@u.northwestern.edu> wrote:

> Thanks for the reply.  I will try it out with phosphorus atoms.
> if you take a look at this image
> http://www.umassmed.edu/faculty/graphics/182/DekkerFig2new.gif
>
> In the way you see above, I'm trying to find a simple way to make a
> straight line (which represents the gene) and pull together the interacting
> regions without having to describe all the x,y,z coordinates because all
> that I need is to be able to define the two regions which are close by (like
> in the image) assuming that all the consecutively listed regions are bonded
> together.
>
> jairav
>
> 2009/4/4 Angel Herráez <ang...@ua...>
>
>> Hello Jairav
>>
>> > The model is meant to be roughly representative, so I just want to
>> > draw a "ribbon" (or rather noodle view where each DNA base is displayed
>> by an atom (to
>> > simplify)
>>
>> Yes. It should work if you set the atoms as phosphorus. I think that Jmol
>> will join them
>> automatically in ribbon or trace mode (it sure does it for alphaC-only
>> proteins).
>>
>>
>> > To make this easier on me, I was wondering if there is a file format for
>> JMOL which uses the
>> > consecutively numbered atoms and assumes bonds between them,
>>
>> Not because the atoms are consecutively numbered. But it will work, as I
>> said, if you use
>> pdb format and put residue numbers.
>>
>>
>> > and then places them
>> > without requiring x,y,z coordinates.
>>
>> I see no way how it can work without xyz coordinates. Everything in Jmol
>> is based on those.
>>
>>
>> > Ideally I'm looking for a way to just put in relative coordinates
>> (distance geometry file for
>> > example).
>>
>> Can you clarify what you mean by that?
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Jmol-developers mailing list
>> Jmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900