My thoughts on Yasara:

I'm jealous!  Yasara is beautiful, fluid, polished, and significantly ahead
of PyMOL in several key technical areas.  To me, Yasara seems like the
"Matrix" of molecular graphics:  its perceptive experience is a quantum leap
beyond PyMOL, VMD, and other conventional programs, and it sets a new
standard for the field.  If you haven't yet tried Yasara on a fast graphics
card (one which supports fragment programs), I highly recommend doing so.
And don't forget to bring the popcorn and soda for those Help Movies!  (PC only, due to use of x86 assembly

The Yasara project was started 5 years before PyMOL, and IT SHOWS. Elmar
Krieger has already done much of the infrastructure work that remains before
us, and from what I've seen, he took the extra time to do things right on
the first pass, whereas with PyMOL, I cut corners in order to get the
software out quickly, fully aware that revision would be required once
additional development resources could be amassed.  

Although Yasara IS revolutionary software, it isn't going to obviate PyMOL
-- PyMOL can still hold its own in a variety of ways.  Plus, given that
there are now over 500 subscribers to the PyMOL mailing list, thousands of
people who use PyMOL, and over a hundred individuals, labs, and companies
that are funding the effort, I am confident that there is *value* and
*staying power* here beyond just sexy images and animations.  

Such benefits take many forms:  graphics quality, robust design, an
efficient user interface, open source code, Python integration, trivial
scripting, cross-platform/cpu support, unrestricted redistribution,
chemistry and crystallography capabilities, an end-user focus, community
momentum, suitability for industry, accountability, overall simplicity,
intuitiveness, a personal touch, and so on.  

Of course, all programs have their own unique strengths.  I'd love to make
PyMOL work more like Yasara and other stellar programs, but only in ways
that specifically matter to you: the PyMOL user community.  So please don't
hesistate to post messages such as Tsjerk's, where you state what you like
about some program, and that you wish PyMOL could do better in those
respects.  You certainly won't hurt our feelings.  Quite the opposite -- you
will earn our gratitude by helping us to improve PyMOL in critical ways.

If PyMOL is to continue succeeding in this crowded environment, we need to
study other good packages and try even to go beyond them, and mostly in
complementary rather than duplicative ways.  Like VMD and PyMOL before it,
Yasara has now raised the bar and upped the ante.  That's good for everyone,
including us.  Here are some key things I noticed that are particularly
inspirational about the Yasara project:

        - Insane performance (60 hz with 15K CPK atoms on the screen?  no
      - Perfect normals and speculars on spheres & cylinders.
        - Use of SDL instead of GLUT for a more polished look and feel.
        - Interactive tutorials.  Simply incredible!
        - Robust animation & texture support.
        - Standardized online documentation.
        - A vector-based programming language (PVL sort of like MOE's

I tip my hat to Elmar -- he is unquestionably one of the most talented
developers around, and his work serves as an inspiration to us all.  Yasara
is already, in certain respects, what PyMOL aspires to become -- but with a
5-year head start, and there are some notable parallels between the two
projects.  Based on his provocative "$100" challenges , Elmar is apparently quite confident
in his current technological lead and is looking to start some friendly
competition.  Well, we'll see...

No doubt some current PyMOL users will switch to Yasara.  So long as you
have sound reasons for doing so, go for it!  I encourage you to use the best
available tool for the problem at hand.  That may mean using PyMOL some of
the time, Yasara some of the time, and VMD, Chimera, VIDA, MOE, CCP4mg,
COOT, O, YAPView, ICMBrowser, Dino, MolMol, RasMOL, Qmol, SPOCK, Cn3D, MAGE,
gOpenMOL, Prepi, Biodesigner, STING, VEGA, or PMV at other times.  

There are now so many choices for viewers, that I do wonder whether there
are truly enough unique needs and opportunities in this area for all of our
efforts to succeed.  

Often I ask: "Is all this gross *duplication* of effort really necessary?"  

A FREE and UNRESTRICTED OPEN-SOURCE viewer should meet the greatest number
of needs for the greatest number of people.  Given all the FREE viewers that
exist, just being FREE and GOOD isn't GOOD ENOUGH in my view.  

Only unrestricted (i.e. non-viral) OPEN-SOURCE software has unlimited
potential to be deployed and enhanced in new and unanticipated ways.  Only
unrestricted open-source software provides you with certainty that your
critical tool won't disappear later on.  FREE, but CLOSED-SOURCE products
like Yasara always have the potential of suddenly vanishing at the whim of
the company, as did Accelrys' formerly FREE version of WebLab/DSViewer.
With such software, you absolutely rely upon the continued mercy and
benevolence of the party which gives the product away.  Is that something
you're willing to risk with the key tools you count on, especially if you
don't have to?

PyMOL is still the only FREE and completely unrestricted OPEN-SOURCE
molecular viewer in its class.  DeLano Scientific cannot take PyMOL away
from you in an attempt to generate revenue, and you do not need special
permission from us in order to use, modify, or redistribute it.  I think
that counts for something, even if PyMOL can't currently match Yasara's
great visual leap forward.  I am confident that given more time and your
continued support, PyMOL will eventually get there too.  


Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: 
> [] On Behalf Of 
> Sent: Friday, April 16, 2004 12:57 PM
> To:
> Subject: Re: [PyMOL] movies in presentations
> Hi,
> I've seen exactly these kind of things happening in a package 
> called Yasara, which is freely available in a limited form at 
> But I am quite fond of the feel and features 
> of Pymol that I would love to see some of such features in 
> there in stead of making the switch :)
> Tsjerk
> On Fri, 16 Apr 2004, Tom Thompson wrote:
> > Mark,
> > 
> > I switched from powerpoint to Keynote and it works much 
> better.  For 
> > example, the beginning of the movie runs much more smoothly 
> now.  BTW 
> > if it matters I make my movies by compressing images in graphic 
> > converter.  About the zoom/stop.  You can have one slide of the 
> > initial frame for the still, then go into the zoom movie (there are 
> > scripts to do this) on the next slide.  Or you could have 
> it all timed 
> > out in one movie to pause for a certain amount of time in a 
> particular 
> > state.
> > 
> > -Tom
> > 
> > 
> > >I'm wondering what software people use to display their pymol-made 
> > >movies to best effect.  I tried embedding the movies in 
> powerpoint, 
> > >but I don't like the performance drop.  Running the movies from a 
> > >movie player like quicktime just doesn't seem integrated enough if 
> > >you want to interact with your movies.  I'm picturing a scenario 
> > >where the movies are seamlessly embedded in the presentation and 
> > >scene-changes can be prompted by a mouseclick.  I know I've seen 
> > >someone do this before, but I don't know what kind of 
> software they 
> > >were using.  I'd like to start with a still image, click my mouse 
> > >have the protein rotate and zoom in on an active site, 
> wait while I 
> > >discuss everything important, then move on to something 
> else when I 
> > >click the mouse again.  In addition, things like labels 
> and text can 
> > >be overlaid over the movies and respond to choreographed 
> mouseclicks as well.  Any ideas?
> > >
> > >- Mark Wilke
> > >
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> -- :)
> -- :)         Tsjerk A. Wassenaar, M.Sc.
> -- :)         Molecular Dynamics Group
> -- :)         Dept. of Biophysical Chemistry
> -- :)         University of Groningen
> -- :)         Nijenborgh 4
> -- :)         9747 AG Groningen
> -- :)         The Netherlands
> -- :)
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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> -- :)         Hi! I'm a .signature virus!
> -- :)         Copy me into your ~/.signature to help me spread!
> -- :)
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