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salilab / imp

The Integrative Modeling Platform
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Use em clustering code to generate coarse structures #566

Closed drussel closed 10 years ago

drussel commented 11 years ago

Should be quite quick to implement.

drussel commented 10 years ago

The current code seems to work well enough.

Pellarin commented 10 years ago

Interesting, what is it?

drussel commented 10 years ago

create_simplified_from_volume and kin. You can play with them using rmf_simplify.

barakr commented 10 years ago

So might be cool to quickly run this tool over a representative dataset of Protein complexes (Benchmark 4.0?). And then publish the DB with a quick and nice paper that shows the utility, in multiscale RMF format. We can add major big complexes - NPC, Proteasome, RNA pol, Ribosome etc., all in RMF in multiscale representation. Also sure to motivate the Chimera guys etc.

Anybody interested? I can join but only with somebody to share the blame for it :) Or if someone wants to go for it on their own, please do, I think it's a cool side project

On Mar 6, 2014, at 8:29 PM, drussel notifications@github.com wrote:

create_simplified_from_volume and kin. You can play with them using rmf_simplify.

— Reply to this email directly or view it on GitHub.

Pellarin commented 10 years ago

Sounds cool! let's speak about that tomorrow!

On Thu, Mar 6, 2014 at 8:59 PM, barakr notifications@github.com wrote:

So might be cool to quickly run this tool over a representative dataset of Protein complexes (Benchmark 4.0?). And then publish the DB with a quick and nice paper that shows the utility, in multiscale RMF format. We can add major big complexes - NPC, Proteasome, RNA pol, Ribosome etc., all in RMF in multiscale representation. Also sure to motivate the Chimera guys etc.

Anybody interested? I can join but only with somebody to share the blame for it :) Or if someone wants to go for it on their own, please do, I think it's a cool side project

On Mar 6, 2014, at 8:29 PM, drussel notifications@github.com wrote:

create_simplified_from_volume and kin. You can play with them using rmf_simplify.

Reply to this email directly or view it on GitHub.

Reply to this email directly or view it on GitHubhttps://github.com/salilab/imp/issues/566#issuecomment-36968263 .

barakr commented 10 years ago

Great! Let's play with it tomorrow over a structure or two, to assess the output. Daniel / anybody, do you know over which structures if any this has been tried? Major params to be aware of that are undocumented?

On Mar 6, 2014, at 9:00 PM, Riccardo Pellarin notifications@github.com wrote:

Sounds cool! let's speak about that tomorrow!

On Thu, Mar 6, 2014 at 8:59 PM, barakr notifications@github.com wrote:

So might be cool to quickly run this tool over a representative dataset of Protein complexes (Benchmark 4.0?). And then publish the DB with a quick and nice paper that shows the utility, in multiscale RMF format. We can add major big complexes - NPC, Proteasome, RNA pol, Ribosome etc., all in RMF in multiscale representation. Also sure to motivate the Chimera guys etc.

Anybody interested? I can join but only with somebody to share the blame for it :) Or if someone wants to go for it on their own, please do, I think it's a cool side project

On Mar 6, 2014, at 8:29 PM, drussel notifications@github.com wrote:

create_simplified_from_volume and kin. You can play with them using rmf_simplify.

Reply to this email directly or view it on GitHub.

Reply to this email directly or view it on GitHubhttps://github.com/salilab/imp/issues/566#issuecomment-36968263 .

— Reply to this email directly or view it on GitHub.

drussel commented 10 years ago

I've just tried it on a handful of pdbs. There is one exposed parameter (the resolution). Internally, there is also the density of the surface sampling. I don't expect that to be very interesting.— Sent from Mailbox for iPhone

On Thu, Mar 6, 2014 at 9:25 PM, barakr notifications@github.com wrote:

Great! Let's play with it tomorrow over a structure or two, to assess the output. Daniel / anybody, do you know over which structures if any this has been tried? Major params to be aware of that are undocumented?

On Mar 6, 2014, at 9:00 PM, Riccardo Pellarin notifications@github.com wrote:

Sounds cool! let's speak about that tomorrow!

On Thu, Mar 6, 2014 at 8:59 PM, barakr notifications@github.com wrote:

So might be cool to quickly run this tool over a representative dataset of Protein complexes (Benchmark 4.0?). And then publish the DB with a quick and nice paper that shows the utility, in multiscale RMF format. We can add major big complexes - NPC, Proteasome, RNA pol, Ribosome etc., all in RMF in multiscale representation. Also sure to motivate the Chimera guys etc.

Anybody interested? I can join but only with somebody to share the blame for it :) Or if someone wants to go for it on their own, please do, I think it's a cool side project

On Mar 6, 2014, at 8:29 PM, drussel notifications@github.com wrote:

create_simplified_from_volume and kin. You can play with them using rmf_simplify.

Reply to this email directly or view it on GitHub.

Reply to this email directly or view it on GitHubhttps://github.com/salilab/imp/issues/566#issuecomment-36968263 .

—

Reply to this email directly or view it on GitHub.

Reply to this email directly or view it on GitHub: https://github.com/salilab/imp/issues/566#issuecomment-36969096