VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Fri Sep 01 2006 - 17:11:55 CDT

Ok.

John Stone wrote:
> Hi,
> Picking is available for graphics objects starting with VMD 1.8.5.
> I've attached an example script that shows how they can be picked
> and reacted to...
>
>
Wow, that's nice!
> Generally speaking, the stuff that would be most beneificial to
> implement as built-in graphics commands are things that you'd generate
> many many instances of in order to draw something useful (which would
> be very slow otherwise), e.g. stuff composted of lots of spheres,
> triangles, etc.
>
Makes sense to me.
> I've been planning on adding mesh primitives (which VMD already has
> internally) which would make rendering of surfaces (used by the
> Intersurf, Intervor, and Virtual DNA plugins) much faster and reduce
> memory use etc.
>
> I don't know what sort of parametric surfaces you have in mind, but
> I wrote an example in the VMD script library that does this:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/3dparplot/
>
>
Never noticed that before, it's fine. I would have expected that is was
more complicated.
> (though the color table code is now out of date... I'll have to update that)
>
And what about changing the material of single objects, not complete
graphics molecules?
Would that be complicated?

Jan
> Splines might be a good choice...
>
> John
>
>
> On Fri, Sep 01, 2006 at 05:52:51PM -0400, Axel Kohlmeyer wrote:
>
>> On Fri, 1 Sep 2006, Jan Saam wrote:
>>
>> JS> Hi John,
>> JS>
>> JS> Here are my two cents:
>> JS> It would be nice to have an arrow, boxes and some sort of parametric
>> JS> surfaces.
>>
>> yep, but at least for arrows, boxes (good point, i'll add that,
>> and square) and alike, i would expect you can usually go
>> without having a graphics version. if those are scripted,
>> the bottleneck should be elsewhere.
>>
>> JS> And splines; I could use splines,too. (I know that VMD is no CAD program
>> JS> but you were asking...)
>> JS>
>> JS> Also it would be nice if materials would be object specific, mot
>> JS> molecule specific.
>>
>>
>> JS> Further a 3D grid maybe even with rulers would be nice.
>>
>> something like that i have actually seen on some of the
>> plugin/script pages linked from the VMD homepage...
>>
>>
>> axel.
>>
>> JS> But what I would like most is if one could pick and move objects so that
>> JS> one does not have to use dummy atoms. Consequently it would also be nice
>> JS> to be able to transform objects using the trans/rot matrices.
>> JS>
>> JS> Jan
>> JS>
>> JS> John Stone wrote:
>> JS> > Going a step further, if people have a need for some of these
>> JS> > additions to run very fast, and they'd get used by a lot of
>> JS> > people's analysis scripts/plugins/etc, I'm willing to consider
>> JS> > creating new low-level drawing commands in VMD to boost performance
>> JS> > if necessary...
>> JS> >
>> JS> > John
>> JS> >
>> JS> > On Fri, Sep 01, 2006 at 10:59:13PM +0200, Jan Saam wrote:
>> JS> >
>> JS> >> Hi Axel,
>> JS> >>
>> JS> >> Good idea!
>> JS> >> Not checking what you have collected already I'm sending a file
>> JS> >> containing 2 or 3 such commands.
>> JS> >>
>> JS> >> Grüße aus der Heimat,
>> JS> >> Jan
>> JS> >>
>> JS> >> Axel Kohlmeyer wrote:
>> JS> >>
>> JS> >>> hi everybody,
>> JS> >>>
>> JS> >>> as many of you might know, the 'draw' command in VMD can be extended via
>> JS> >>> providing procedures of the name vmd_draw_XXX, which would be turned into
>> JS> >>> a draw XXX command. the general idea is to provide an option to
>> JS> >>> overide the
>> JS> >>> internal graphics command and intergrate compound objects built from the
>> JS> >>> povided primitives. there is one example in the user's guide and i've
>> JS> >>> started
>> JS> >>> building some more, while at the same time making them as similar as
>> JS> >>> possible
>> JS> >>> to the internal graphics commands (and thus the default draw commands).
>> JS> >>> the result is currently at:
>> JS> >>> http://biocore.ks.uiuc.edu/biocore/biofs/VMD%20(Public)/src/rpm/vmd_draw_lib.tcl
>> JS> >>>
>> JS> >>> and can be used by copying it into $VMDDIR/scripts/init.d/ or using the
>> JS> >>> contributed rpm(s).
>> JS> >>>
>> JS> >>> i'm currently looking for additional implementations of those kind of
>> JS> >>> compound
>> JS> >>> draw objects, so that i know what is used and needed and that we can have
>> JS> >>> a reliable and consistent library of those scripts that could be
>> JS> >>> shipped with
>> JS> >>> vmd at some point in time and that script or plugin writer can depend on
>> JS> >>> (and thus do not have to reinvent that wheel over and over again).
>> JS> >>> don't worry, if your draw extension is not written as elaborately as the
>> JS> >>> ones provided in the library so far, i'm more interested to see what
>> JS> >>> other
>> JS> >>> people want/need and some kind of prototype implementation.
>> JS> >>>
>> JS> >>> best regards,
>> JS> >>> axel.
>> JS> >>>
>> JS> >>>
>> JS> >> --
>> JS> >> ---------------------------
>> JS> >> Jan Saam
>> JS> >> Institute of Biochemistry
>> JS> >> Charite Berlin
>> JS> >> Monbijoustr. 2
>> JS> >> 10117 Berlin
>> JS> >> Germany
>> JS> >>
>> JS> >> +49 30 450-528-446
>> JS> >> saam_at_charite.de
>> JS> >>
>> JS> >
>> JS> >
>> JS>
>> JS>
>>
>> --
>> =======================================================================
>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
>> Center for Molecular Modeling -- University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>> =======================================================================
>> If you make something idiot-proof, the universe creates a better idiot.
>>
>
> 

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de