Macromolecular Modeling Blog ™

Hi there,

I really think this is a great idea and I am looking forward to joining your webinar.

Best
Jan

Will be exciting to participate in Rosetta Design workshop sitting at own workplace.

Yes it is a good idea to arrange such a webnair but at the same time it is really a bad idea to not make it free.

Hi Imtiaz-

We would love to make it free but at this time we do not sell Rosetta licenses (nullifying the promotional aspect, Rosetta itself is in fact is free to academics) nor would we have any other source of funding to cover the costs (like advertising or grants). We could apply for a government grant to cover the costs of the webinar but it would take >9 months to receive the funding (if we get funded!). We want to do the webinar because of the strong demand and as a learning experience for us as well. We are currently figuring out pricing (based on projected interest) but I can tell you that at best we will be covering our costs and more likely we will be losing money on the endeavor. I’m happy to pose the question (and follow through with the answers)- do you want to wait >9 months with a ~50%(?) chance of having a free academic workshop?

If anyone (e.g. potential sponsors?) has other suggestions about making the workshop “free”, please email us.

Great idea to have a webinar!

Thanks for the materials. It was a dense webinar for those not so familiar with the docking protocols (like me). I hope I will now be able to review the examples carefully and, above all, analyze the output of every example to grasp the full potential of the various protocols.

Hi,
the webinar has been very useful to make solid what we learned from the (incomplete) rosetta manual. This gave us confidence that we were doing things correctly.

However, the ensemble and loop rebuild parts should be improved, since these are parts that are very poorly documented in the manual.

1) The ensemble example is great to run docking-ensemble, but it misses the ensemble_prepack step. We spent 2 frustrating weeks, but we haven’t found the correct keys combination. Can you help on this ? Posting the command line here or on the rosetta forum ? An example is useful if it gives a recipe from start to the end.

2) Adding a similar example (start to end) for docking with loop rebuild would be really great.

Hi Luigi,

I’m glad the webinar was useful. We appreciate all of the positive feedback. A tremendous amount of work went into this webinar and our reward is learning that we may have taken the edge off of RosettaDock for our participants.

1) I have added an ensemble_prepack directory to the demos which has a command line and all of the input files needed to generate the ppk files used in the ensemble docking example.

2) There is a docking with loop rebuilding tutorial provided in the demos (see 6-flexible_backbone). It is a fairly simple example but it should give you a place to start. To add more loops in the example, you would just append additional lines for every additional loop to the t000.pose_loops file.

Unfortunately, it does not cover the process of creating the needed fragment libraries. We could give an entire presentation and tutorial on creating fragment libraries (which we’ve done many times!). If we give a webinar on ab initio, we would go over fragment library creation. In the meantime, there is some documentation at:

http://www.rosettacommons.org/tiki/tiki-index.php?page=Fragments

Xavier,

that’s really great! We understand that behind this webinar and rosetta in general there is a huge amount of work. However, 5 minutes from some of you can save days to lot of people around the world, and make the rosetta community grow.

Thanks again,
Luigi

So, any plans to make another webinar, for those who missed the first one?

it is a great idea. And I am wondering if there is any chance to download webinar’s materials for people who wasn’t able to “attend”? or maybe it is the time to do a next one?

Hi there,

Are there any plans for webinars on basic Rosetta available to non-academic users?