[PyMOL] PyMOL manual
My advice is not to try to figure out all this stuff by yourself, but rather to try the new demos and then ask questions via the mailing list. Or, simply wait until I get some time later this month or next to update the documentation. T Warren, I thought you had recently hired a writer to work up a PyMol manual? How is this going? Do you have a projected release date for the new manual? Thanks, Scott == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular & Cell Biology 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ==
RE: [PyMOL] PyMol Manual
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. 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. 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. 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: gwebs...@lexigenpharm.com [mailto:gwebs...@lexigenpharm.com] Sent: Monday, October 28, 2002 10:33 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMol Manual Fellow PyMol Users Although I like using PyMol, I would like to submit a gripe about the severe lack of a decent PyMol manual. 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) 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. 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. A good, clear and well-thought out manual really helps to make a case for using a particular piece of software (an
Re: [PyMOL] PyMol Manual
Dear Byron Yes, it's a nice Catch-22 isn't it ... write a PyMol manual so people like myself will be able to learn PyMol well enought to be able to write the PyMol manual! Gordon Byron Delabarre 10/28/2002 01:32 PM Please respond to byron To: gwebs...@lexigenpharm.com cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMol Manual So write one. gwebs...@lexigenpharm.com wrote: > > Fellow PyMol Users > > Although I like using PyMol, I would like to submit a gripe about the > severe lack of a decent PyMol manual. > > 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) > > 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. > > 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. > > 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"). > > Gordon > EMD Lexigen Research Center -- Byron DeLaBarre Stanford University / HHMI Dept. of Molecular and Cellular Physiology P250 MSLS Building//(L)650 736 1714 (C)650 468 5677
Re: [PyMOL] PyMol Manual
So write one. gwebs...@lexigenpharm.com wrote: Fellow PyMol Users Although I like using PyMol, I would like to submit a gripe about the severe lack of a decent PyMol manual. 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) 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. 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. 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"). Gordon EMD Lexigen Research Center -- Byron DeLaBarre Stanford University / HHMI Dept. of Molecular and Cellular Physiology P250 MSLS Building//(L)650 736 1714 (C)650 468 5677
[PyMOL] PyMol Manual
Fellow PyMol Users Although I like using PyMol, I would like to submit a gripe about the severe lack of a decent PyMol manual. 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) 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. 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. 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"). Gordon EMD Lexigen Research Center