- This topic has 2 replies, 2 voices, and was last updated 9 years, 6 months ago by Anonymous.
May 31, 2014 at 12:28 pm #1900Anonymous
I found someone had solve a difficlut proble by combine the rosetta with phenix, which can help calculate the x-ray structure with low resolution.
So I want to copy this as well to solve my problem, and I found a way to combine rosetta with phenix. Here is the website about phenix.rm_rosetta:
To combine them, I need the resource code of rosetta.
“You must obtain a separate license for Rosetta, which is free for academic users. The software is primarily distributed as source code, which will be linked to Phenix as part of the install process. Once you have obtained and unpacked the Rosetta distribution, the top-level directory should have a sub-directory called “main”, containing additional sub-directories “source” and “database”. You should first set environment variables to tell Phenix where to find the Rosetta distribution, and tell Rosetta where to find the database files, for example:
To get the latest version of rosetta, I acquiered a licence on “UW Center for Commercialization” for academy use only. And they send me a link to download the rosetta software.
However, when I got the latest version for my mac, “PyRosetta.MacOSX.Lion.64Bit.release-r14.tar.bz2”, I unpacked it and found that there is no folder called “main” and what I got is none source code at all. The “readme.txt” showed that there is no need to install rosetta, what I should do is just to execute it for use.
So my problem is: how can i get the source code? Did I do anything wrong? Got the wrong website? Downloaded the wrong file or wrong version? Or there is some other folders to replace the folder of “main”? Did anyone succeed in combine phenix and rosetta to get the “phenix.rm_rosetta”?
Thanks for your attention, and I really appreciate it if someone can give me an advise.
June 3, 2014 at 6:39 pm #10074Anonymous
There’s a difference between the PyRosetta download and the regular Rosetta release. They’re both based on the same code base, but the way they are built and used are different. (And are licensed seperately.)
I’m not 100% sure, but from the Phenix documetation it looks like it’s asking you to download and install the regular (non-PyRosetta) version of Rosetta. To do so you would go to http://c4c.uwc4c.com/express_license_technologies/rosetta (the link in the Phenix documentation labeled ” separate license for Rosetta”). Don’t click on the link for PyRosetta, but instead look further down the page and click on the appropriate “Academic License” or “Commercial License” button on that same page. You’ll eventually get an email with details on your user name and password to download Rosetta, and a link to the download page. (Should be also availible through https://www.rosettacommons.org/software/license-and-download)
Any of the “weekly release” builds should contain the “main” directory. (Don’t attempt to use Rosetta 3.5 or Rosetta 3.4 – they’re older and the layout is different. )
June 6, 2014 at 5:57 am #10083Anonymous
Yes, so you are wright. I can find the exact version now. Thank you very much. What you said is really useful. There are two different versions. One is just the software for use called PyRosetta, the other is Rosetta Suite with the folder named “main”. Thank you again.
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