Re: [ccp4bb]: Re: your mail

["Warren L. DeLano" <warren@sunesis.com>]

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I'd like to avoid a flame war, but it's worth distiguishing O, oops2, and
similar packages from modern systems like PyMOL.  This is really an
"apples to oranges" comparison.  Specialized tools like oops2 are the best
solutions today for performing most crystallographic tasks, and that's not
going to change overnight.  Eventually however, it will change.

Packages like PyMOL fuse standard, widely-used software  architectures
(such as Python) with crystallographic and molecular 
computation.  Straight out of the tarball or ZIP file, PyMOL can't do
nearly as much structural biology as traditional packages, but with a
surprisingly small amount of script writing, PyMOL can be extended to meet
or exceed existing solutions for many tasks.  As with O macros, the
simplicity of Python means that end-users can quickly customize or add new
functionality into PyMOL.  

However, one notable difference is that solutions built using O macros can
only be used on machines with valid O licenses, whereas solutions built
using PyMOL can be shared and used by anyone, anywhere, and without
cost.  Furthore, to use systems like PyMOL, cctbx, Birdwash, and PMV, you
only have to learn one common scripting language: Python. 

In general, Python is far more advanced and capable than the O macro
language, but that hasn't mattered until now since Python lacked suitable
functionality in key areas.  By providing Python with support for
models, maps, symmetry, and molecular editing, PyMOL endows Python with
the functionality it needs in order to start competing with the O macro
language for certain visualization operations.  It isn't perfect, but it
is a good start.  Birdwash apparently does this as well (but is still in
alpha development).

Over time, solutions built using Python will gradually displace
existing packages in niche areas, and the cumulative effect of this will
be to make PyMOL and similar packages into the preferred platforms for
molecular computation, including crystallographic model building.  I'd
argue that PyMOL is already the best choice for easy publication-quality
figure generation.

Power-users who want to customize packages or even develop new
tools should consider whether it makes more sense to use rich, mature,
but closed and isolating approaches (such as O macros, standalone FORTRAN
code, or Molscript, Grasp, X-PLOR, and CNS scripts) versus lean, immature,
but open and highly interopable alternatives (such as Python scripts which
drive PyMOL, cctbx, and similar packages).  

DVD has a good point.  If you want everything today, use his wonderful
tools!  But if you want to build and use even better tools for the future,
then start thinking about adopting open, interoperable alternatives as
soon as they are capable of meeting your needs.

- Warren

On Sat, 8 Dec 2001, Gerard "DVD" Kleywegt wrote:

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> > > > >  I am wondering if there is way to automatically walk through a
> > > > protein
> > > > > structure from N-terminal to C-terminal, so to have a better sense of
> > > > 
> > > > > chain trace than the ramp painting?
> > > > 
> > > > isn't this what you do when you rebuild your protein ? you can use OOPS2
> > > > to
> > > > generate O macros to take you from one residue to the next; see the
> > > > manual at
> > > > http://xray.bmc.uu.se/usf/oops2_man.html
> > 
> > If you'd prefer to use a robust scripting language like Python instead of
> > O macros, you can do the same kind of thing with PyMOL.  After loading a
> > structure, run "walk.py" below to be able to walk the chain using the F1
> > and F2 keys.  It could easily be customized to suit your needs.  
> 
> but on the other hand, if you think that python is a british comedy show and
> you don't even want to know what a 'robust scripting language' is, you can
> always simply put "ce_nex ;; CA" (centre_next) on your O menu - every time you
> click it you go to the next residue (and centre_prev will take you back)
> 
> however, if you *are* interested in producing protein *models* that are robust
> (e.g., in the sense that they won't show up as an entertaining example a paper
> about validation or protein model quality), you might still want to check out
> oops2, even though it's written in fortran and produces humble little O
> macros.
> 
> oops2 enables you to do something rather more interesting than generating a
> trivial walk through your model. it can instead be used (if you want) to
> generate a residue-by-residue critique of your model (including such things as
> ramachandran violations, poor real-space fit, what-if-generated errors, etc.).
> you can choose to walk through your entire model or only visit the residues
> that violate at least one criterion, and you can do it from first to last
> residue or starting with the residue with the largest number of violations
> (the latter is a convenient way for busy supervisors to check that the models
> they are about to attach their name to and write a paper about are actually
> supported by the experimental data and look protein-like ...). for every
> residue visited, a macro or set of commands can be executed automatically
> (e.g. contouring your maps, generating symmetry-related molecules, etc.).
> oops2 can not only reduce the time you spend checking and rebuilding your
> model, it also focusses your attention on those residues most likely to need
> it.
> 
> --dvd
> 
>   (who hates to admit that he has actually written some java code recently)
> 
> ******************************************************************
>                         Gerard J.  Kleywegt
>     [Research Fellow of the Royal  Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology  University of Uppsala
>                 Biomedical Centre  Box 596
>                 SE-751 24 Uppsala  SWEDEN
> 
>     http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
> ******************************************************************
>    The opinions in this message are fictional.  Any similarity
>    to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
> 
> 
>