Bob,
I've had a play MoveTo and it's clearly got lots of potential but is not
quite what I had in mind. Currently I'm using jmol to provide a web view
on our in house archive of X-ray structures although I've got some other
ideas longer term. It's uses perl cgi in the background so that
structures appear on the website as soon as they're saved to the archive
area resulting in an essentially sef-maintaining site. From a jmol
perspective it's fairly basic but I've added a few buttons to switch
commonly used viewing modes like ribbons and also to zoom on the
inhibitor. Finding an inhibitor in a protein you don't know well is
suprisingly difficult but something as simple as:
select not protein and not solvent;
center selected;
zoom 1000;
wireframe 0.2;
Is quite helpful but "zoom (not protein and not solvent)" could be even
better.
I'm not sure how easily I could use MoveTo for the variety of structures
present in the archive without loosing the self-maintaining aspect of
the database.
I think I also agree with Frieda's comments. The behaviour which gives
the script author the most control is to be prefered and it's up to them
to use a sharp tool corectly. One place where it might be nice to fail
safe is if "selected" equates to nothing in which case nothing should
happen. There are apo (no ligand) structures in my archive which I'd
otherwise have to test for.
Kevin Parkes
> Message: 5
> From: Frieda Reichsman <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] More on zoom
> Date: Mon, 10 Apr 2006 11:37:42 -0400
> To: jmol-users@lists.sourceforge.net
> Reply-To: jmol-users@lists.sourceforge.net
>
>
> --Apple-Mail-31-1020021332
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
> charset=US-ASCII;
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>
> On Apr 10, 2006, at 8:30 AM, Bob Hanson wrote:
>
> > It's on the agenda for post-10.1. It will probably be:
> >
> > zoom (selected)
> > zoom (not protein and not solvent)
> >
> > etc.
> >
> > But this is trickier than you might think because of the way
> > perspective depth is handled. Thus, to work the way you expect,
> > this command might require
> >
> > set perspectiveDepth OFF
> >
> > There are all sorts of issues here.
>
> Not sure if you want answers to the following, but to me they seem
> straightforward...
> >
> > What if someone says the following?
> >
> > zoom (atomno=30)
> >
> > Do we see one big dot?
>
> Yes - the author will have to script an atomset, not just an atom,
> into the zoom to avoid that.
>
> > Is there some sort of maximum zoom just for this command?
>
> No.
>
> > Does it recenter the model in the window at the center of
> that group?
>
> Not unless I want it to... i.e., tell it to.
>
> > Should it the center of rotation as well?
>
> Ditto.
>
> These behaviors give the author the most control, which to me is
> desirable.
>
> Frieda
>
>
>
> ///////////////////////////////////////////
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures http://www.moleculesinmotion.com
>
> ///////////////////////////////////////////
>
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