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

2012-06-15 Thread Jason Vertrees
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 shane.nee...@gmail.com 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


 --
 Live Security Virtual Conference
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 threat landscape has changed and how IT managers can respond. Discussions
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: [PyMOL] 60-mer virus capsid (need computing power!)

2012-06-15 Thread Shane Neeley
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 
jason.vertr...@schrodinger.com 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 shane.nee...@gmail.com
 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
 
 
 
 --
  Live Security Virtual Conference
  Exclusive live event will cover all the ways today's security and
  threat landscape has changed and how IT managers can respond. Discussions
  will include endpoint security, mobile security and the latest in malware
  threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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  Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrödinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
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Re: [PyMOL] 60-mer virus capsid (need computing power!)

2012-06-14 Thread Tsjerk Wassenaar
Hi Shane,

I've been playing with a virus 60mer on an intel core i7 workstation with
6Gb memory with good response. Just make sure you use the latest incentive
or open source version and have a good graphics card.

Cheers,

Tsjerk

On Jun 14, 2012 11:49 PM, Shane Neeley shane.nee...@gmail.com 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/Ahttps://mail.ohsu.edu/owa/redir.aspx?C=a84e20fef7e04111bec08a76775f0093URL=http%3a%2f%2fstore.apple.com%2fus_smb_78313%2fconfigure%2fMD771LL%2fA

Has anyone built other machines to do this sort of work?

Appreciate your input,

Shane Neeleu


--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
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