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Message boards : GPUGRID CAFE : Visualisation

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ChristianVirtual
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Message 37587 - Posted: 16 Aug 2014 | 6:16:33 UTC

Are there any visualisation tools around to display the molecules processed in a task for GPUgrid ? Similar to other DC projects ?
Would the data be available to developer of 3rd party tools ?

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Message 37690 - Posted: 20 Aug 2014 | 0:02:18 UTC

As I know there is no way for us to see the processed molecules. And probably there won't be, it is said the visualisation will use gpu resources and slow the crunch speed.

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Message 37694 - Posted: 20 Aug 2014 | 12:41:27 UTC - in response to Message 37690.

too bad; even more as the visualisation could be done on a different system; like a tablet ...

I find it rather interesting to see the proteins I'm working on; just from aesthetics point of view they but also to learn more about the science.

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Message 37697 - Posted: 20 Aug 2014 | 16:32:18 UTC - in response to Message 37694.

Not as a BOINC screen saver, but you certainly can view the structure - look for the structure.pdb file in the slot directory, open it in notepad and get the "soft_link" path to the real file. You can then open that in the viewer of your choice - I recommend VMD http://www.ks.uiuc.edu/Research/vmd/

Matt

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Message 37717 - Posted: 22 Aug 2014 | 22:43:55 UTC - in response to Message 37697.
Last modified: 22 Aug 2014 | 23:02:56 UTC

Great; thanks ! Thats exactly (!) what I was looking for. Great starting point for my plan. Hell, they even still have the water in ...

Do you know by chance if there is also information about the bonds; it could be recovered from the PDB file seems but might be hidden in some other file (grep'ed but nothing found)

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Message 37722 - Posted: 23 Aug 2014 | 17:21:49 UTC - in response to Message 37717.

The bonding information is in a different file, the format of which depends on the type of simulation. VMD, and pretty much all other viz programs are smart enough to infer bonding, based on proximity (it's not perfect, but it's adequate for viz). If you're rolling your own, you can assume that any atoms within about 2A of one another are bonded. (PDB coords are in Angstrom)

Matt

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Message boards : GPUGRID CAFE : Visualisation