RE: [PyMOL] different transparencies

2003-03-16 Thread DeLano, Warren
CC'd to list for future reference...

Michal,

For mixed colors, you need to use the same trick (separate objects). 
However, if you want the spheres to have a uniform color, in which case you can 
set sphere_color,white etc., without having to create separate objects.

PyMOL's internal raytracer isn't likely to support perspective any time 
soon.  Instead, I recommend using PovRay.

Cheers,
Warren

 Subject: Re: [PyMOL] different transparencies
 
 DeLano, Warren wrote:
 
 Because of the way settings work in PyMOL, you will need to 
 split your spheres into different objects in order to get 
 this to work.
 
 Try the following script:
 
 load $PYMOL_PATH/test/dat/pept.pdb
 create cpy,pept
 hide
 show sph,pept and name ca
 show sph,cpy and name n
 set sphere_transparency,0.5,pept
 ray
   
 
 Hi Warren.
 Thank you for hint. Excuse me I reply directly, but I think 
 you are the 
 best information source in this field. Could you hint me also how to 
 hack if I want to have different color for sphere and sticks 
 belonging 
 to the same atom (I want to use transparent sphere colored by element 
 and black sticks).
 I wonder if built-in raytracer can render in perspective mode in near 
 future.
 
 Regards,
 Michal Bozon
 
 Cheers,
 Warren
 
 
   
 
 I would like to have some spheres transparent, but some 
 spheres leave 
 opaque. Or to have spheres with different transparencies. Is 
 it possible?
 
 Thanks,
 
 Michal Bozon
 
 
 
 
 



[PyMOL] A New Phase for PyMOL

2003-03-16 Thread DeLano, Warren
Dear PyMOL Users and Friends,

It is with great excitement and anticipation that I announce a new 
phase for PyMOL:  Beginning April 3rd, 2003, I will be committed FULL-TIME to 
the development, documentation, and support of this Open-Source package through 
my limited liability company, DeLano Scientific LLC.

This step is made possible through financial sponsorship received from 
a small group of PyMOL users during the past 18 months.  Thank you very much 
for that.  Your backing has given me the courage to launch even in these 
uncertain times.  Don't let terrorism, recession, war, or epidemics dissuade 
you -- you only get one life in which to pursue your dreams!

Fortunately, my five-year relationship with Sunesis Pharmaceuticals 
continues on good terms, and the company will remain an active test site for 
PyMOL though I will no longer be an employee.  All of us owe Sunesis a debt of 
gratitude for nurturing the development of this package over the past several 
years. 

PyMOL now enters a critical time.  We absolutely must secure additional 
funding in order to sustain our activities.  While we hold out hope for a large 
influx from big pharma, so far it has not yet materialized.  Nevertheless, 
because we are starting out small and efficient, we can succeed this year 
mainly on grass-roots academic and small-company sponsorship if each of you 
takes the initiative within your organization to support PyMOL.

Thus, I urge every user to advocate for purchase of a PyMOL license and 
maintenance subscription for their group now that the package will be supported 
with rapidly improving documentation, responsive feedback, and regular updates. 
 If you sponsored the project in 2002, then please consider renewing your 
maintenance subscription in 2003.  

http://www.pymol.org/funding.html

Though PyMOL will always be unrestricted Open-Source software, DeLano 
Scientific will also be rewarding sponsors with extra perks known as Incentive 
Products.  These will soon include an expanded manual and protein morphing 
capability, and will eventually enable electrostatic calculations, sequence 
editing, direct movie output, a molecular force-field, and on-site training.  

Please understand that my aim is to keep the package as open as 
possible while adopting a reliable strategy for paying the bills.  Without 
incentives, we find that only about 5% of users contribute.  If PyMOL is to 
eventually surpass the capabilities of traditional commercial products, we need 
to secure sponsorship from a majority of users.  Hence this compromise.

More details will follow in coming months.  If you wish to know more 
about DeLano Scientific and our software philosophy, then please follow this 
link:

http://www.delanoscientific.com/about.html

Cheers,
Warren L. DeLano, Ph.D.
war...@delanoscientific.com