RE: [PyMOL] PyMol Manual

[DeLano, W. <wa...@su...>]

Gordon,

    I fully agree with your assessment that PyMOL is currently unable to =
reach its potential due to a number of factors, including poor =
documentation.=20

    Nevertheless, I do have a defined plan for eliminating these =
deficits.  It involves securing funding to hire people under contract to =
document, support, and develop PyMOL on an ongoing basis.  While I am =
grateful for the continued assistance of PyMOL users on numerous minor =
tasks, it is not reasonable to expect anyone to prepare a complete =
"well-written" manual or to perform other major tasks without some form =
of compensation.  Also, PyMOL is still immature enough in certain areas =
that a full manual really can't be constructed until the 1.0 features =
are settled upon (soon hopefully!).

    Understanding this situation, several large pharmaceutical companies =
and many smaller entities have lent support to PyMOL development through =
donations and license purchases.  At present the flux is low, but we are =
getting to a point where some real headway can be made.  The forthcoming =
"Incentive PyMOL (iPyMOL)" add-on will hopefully increase the flux by =
providing a specific reward to those who fund the PyMOL development =
effort. =20

    I know it may sound like PyMOL/iPyMOL is becoming commercial =
gray-ware, but that's not it at all.  I haven't devoted thousands of =
hours to this project just to see it end up as yet another expensive, =
lousy, inflexible, and closed-source commercial tool.  PyMOL will remain =
a vital open-source project, and iPyMOL will exist solely to accelerate =
PyMOL's growth and guarantee its long-term health.  Nurturing PyMOL and =
similar efforts to fruition on such terms is central to my career vision =
-- it's what I stand for in this industry.

    I believe that well-supported, well-documented, and well-maintained =
open-source software will be a superior research product to what is =
currently offered by the major scientific software vendors.  My hope is =
that scientists in industry and academia will eventually come to =
appreciate this, and then choose to make creation of such software =
economically viable through funding of balanced approaches such as the =
one I am taking with PyMOL.

    Free software is great once it exists, but there are far too few =
developers in this field to expect the kinds of dramatic successes =
achieved by the Linux, GNU, and BSD communities.  If =
open-source/free-software is going to have a large impact on molecular =
modeling, it will need direct support from users, universities, =
governments, and for-profit companies.  If really good open-source tools =
were available and able to meet the needs of research, would you be =
willing to pay reasonable amounts of money for their development, =
maintenance, and support?  I hope so.

    Thus, pharmaceutical companies like EMD/Lexigen/Merck can choose to =
continue to spend millions of dollars on traditional closed-source =
packages with no hope of a reprieve, or they can choose to funnel a =
small fraction of that money into efforts like PyMOL.  Over the long =
term, open-source packages offer vendor-independence, =
cost-effectiveness, flexibility, opportunities for innovation, and =
support for broad sharing of information and technology.  These are all =
key ingredients in scientific progress, both within a single =
organization and across the industry. =20

    Realistically, it will take a year or more before PyMOL can fulfill =
the potential you described.  How soon this happens will depend in part =
on whether people like yourself are content to merely gripe about the =
status quo, or whether you are prepared to commit resources towards =
improving it.

Cheers,

Warren L. DeLano, Ph.D.
PyMOL Creator &
Founder, DeLano Scientific

-----Original Message-----
From: gwe...@le... [mailto:gwe...@le...]
Sent: Monday, October 28, 2002 10:33 AM
To: pym...@li...
Subject: [PyMOL] PyMol Manual



Fellow PyMol Users=20

Although I like using PyMol, I would like to submit a gripe about the =
severe lack of a decent PyMol manual.=20

A deeper description of the program's features is required if people are =
seriously going to use PyMol for tricky things beyond simple =
visualization (simple visualization programs are ten-a-penny and PyMol =
could be so much more)=20

Particularly lacking are details of structural editing (mutation, bond =
rotation, cut-and-paste etc.), interfaces (if any exist) to routines for =
enegy minimization and a detailed description of the Python command line =
interface with examples of scripting and how to extend PyMol's =
capabilities.=20

By neglecting to adequately document what may be a really useful =
program, the PyMol user community might fail to attract the kind of user =
base and support that it deserves and that it needs to ensure its =
success.=20

A good, clear and well-thought out manual really helps to make a case =
for using a particular piece of software (and it might also lower the =
odds of PyMol having to join the gray legions of commercial "payware").=20

Gordon=20
EMD Lexigen Research Center=20