Re: [PyMOL] 60-mer virus capsid (need computing power!)

[Shane N. <sha...@gm...>]

Hi Jason,

Thanks a lot for the performance info. I think that a full capsid would be
around 300,000 atoms, so your info is very helpful.

We will probably invest in the newest version of pymol when we purchase the
computer.



On Fri, Jun 15, 2012 at 12:19 PM, Jason Vertrees <
jas...@sc...> wrote:

> Hi Shane,
>
> With PyMOL v1.5 and later, and a reasonable machine you should be able
> to use large systems (>250,000, and upward of 1,000,000+ atoms)
> without much of a problem. Using the following simple test script:
>
> fetch 2xpj, type=pdb1, async=0
> split_states 2xpj
> delete 2xpj
> orient
>
> For these 240,000 atoms on a Dell T5500 with a very nice video card, I get:
>  * 30 FPS as lines
>  * 28 FPS using cartoons
>  * 30 FPS a ribbons
>  * 30 FPS as surface
>
> For these 240,000 atoms on a (1 year old) MacBookPro (with ATI Radeon
> HD 6770) I get
>  * 60 FPS as lines
>  * 33 FPS as cartoon
>  * 36 FPS as ribbon
>  * 27 FPS as surface
>
> 30--60 FPS is surely in the realm of "interactive". Earlier versions
> of PyMOL would have a tough time with these data. (Plus the new
> versions of PyMOL have nicer rendering in real time.)
>
> Next, you wrote:
>
> > Is a 12-core mac like this overkill?
> > http://store.apple.com/us_smb_78313/configure/MD771LL/A
>
> With Moore's Law still in effect, nothing is overkill. However,
> consider value for money: the recent announcements from Apple centered
> around the MacBookPro -- not the MacPro.
>
> It should be clear that those who financially support PyMOL are
> responsible for this level progress. The diff from v1.4 to v1.5 was in
> the range of 50,000+ lines -- and we couldn't have done that work
> without our supporters. So, a special thanks goes out to them!
>
> Cheers,
>
> -- Jason
>
>
> On Wed, Jun 13, 2012 at 2:32 PM, Shane Neeley <sha...@gm...>
> wrote:
> > Hi,
> >
> > Does anyone use pymol for very large structures, such as a full virus
> 60-mer
> > capsid? If so, what processing power, memory, graphics card, etc. do you
> > need to render these large files and manipulate them without any slowing?
> > PyMol takes about 1 minute to think after trying to spin one of these
> full
> > capsids, and that is on a dual-core 8gb ram laptop.
> >
> > Is a 12-core mac like this overkill?
> > http://store.apple.com/us_smb_78313/configure/MD771LL/A
> >
> > Has anyone built other machines to do this sort of work?
> >
> > Appreciate your input,
> >
> > Shane Neeleu
> >
> >
> >
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>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>