Re : installation of rosetta 3.0 on fedora core 6

[Anonymous]

Hi,

I am new to rosetta .. I have downloaded and installed rosetta 3.0 on fedora core 6 platform .. I gave the commnand scons bin mode=release, being in the rosetta3_source directory.. as it was complied wihtout any errors.. but i don’t know how to use it for any procedure .. after checking the manual .. I followed some steps and being in the loopmodeling directory rosetta3_demos I gave the following command :-

loopmodel.linuxgccrelease -nstruct 1 -database /home/sriram/Desktop/rosetta3/rosetta3_database -loop::/home/sriram/Desktop/rosetta3/rosetta3_demos/LoopModeling/inputs/4fxn.start_001.pdb

Its giving the error : loopmodel.linuxgccrelease: command not found

Actually I am a bit confused about using it .. can anybody help me .

[Anonymous]

I solved the problem by setting the path to the bin directory .. but I want know one thing that If I want to use a fragment library of 10 residues or above how can I create it also … is it possible to use 10 fragment library to model the loop as I was reading the following paper – .

Hu X, Wang H, Ke H, Kuhlman B.

Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
Abstract

In this paper they have used a library of fragments of size 10 and designed the loop using rosetta only.. if anybody can shed some light on this topic it will be of great help

[Ora Furman]

That paper was done 4 or 5 years ago, so it’s in the very old version of Rosetta++. The functionality is not imported into the 3.* version, but I think the new 3.* version loop modeling protocol should be more powerful and flexible. If you still decide to use the old protocol, you’ll have to install the old version and I can show you the command line.

[Anonymous]

Hi,

A) Did you really mean Rosetta 3.0? I strongly suggest upgrading to 3.2.

That paper was done in Rosetta++ (one of the 2.x versions). The precise protocol was never ported from 2.x to 3.x. I’ve asked the authors what they think about getting it done in either version.

C) The hardest part is likely to be the fragments. The easy way to generate fragments is with the robetta server (http://robetta.bakerlab.org/), but it only makes 3mers and 9mers. You’ll need to learn to make your own fragments to get 10mers. The old-style fragment generating code is included with 3.2; there is also a powerful fragment picker included inside 3.2. Unfortunately I know how to use neither of these.

D) The existing loopmodeling executeable is not set up to perform design, but that can be changed in a relatively straightforward fashion. It may be easier for you to write your own script (using the RosettaScripts tools) than change loop modeling, it will be your choice.

[Anonymous]

Actually I tried installing rosetta 3.2 first ..but I was getting errors so I installed rosetta 3.0 … As u have recommend to use 3.2 I will try to install again and if some errors arises I will get back to u ..
Also I want to ask that if we already have a database of fragments and I reorder it according to the 9 mer format of rosetta library would it be possible to use it .. and if yes how ??
I didnot understand the first part of ur last question… I don’t want any loop designing … What I want is to pick a fragment from a fragment library of say 10 residues and model the loop for the defined region and gives the model without any much structural changes to the backbone of the protein … Since after getting the best model I have to test it in wet lab whether the protein is active or not after the new loop insertion ??

I would like to ask one more thing … Can u refer me to some detailed manual or paper where I can find everything about rosetta since I find it quite amazing for doing such jobs and I want to learn more and have a firm grip on it .. also I am not a programmer in python though I know perl .. but I have started learning python to code for my own stuff … so any good reference will help me a lot..

Thanks

[Anonymous]

“Also I want to ask that if we already have a database of fragments and I reorder it according to the 9 mer format of rosetta library would it be possible to use it .. and if yes how ??”

I don’t quite understand the question. If you already have fragments, then I’m sure you can transform them from one format to another to get rosetta to like them. I don’t know how to do it, and I’m not aware of any fragment-converting scripts out there, I guess you’ll have to writeone.

“I didnot understand the first part of ur last question… I don’t want any loop designing … What I want is to pick a fragment from a fragment library of say 10 residues and model the loop for the defined region and gives the model without any much structural changes to the backbone of the protein … Since after getting the best model I have to test it in wet lab whether the protein is active or not after the new loop insertion ??”

If you are not designing, then what is there to test? Fragment insertion is generally constant-sequence, and if you don’t change the sequence then what is there to test in the wet lab?

Do you mean, you want to insert the fragment’s sequence along with the fragment itself? That is possible with the newer fragment code in 3.2, but an application to do it that way has never been written. The loop modeling executeable won’t do it. There’s code in development that shows it is possible, but we don’t expect it to be finished for another year or so.

The most recent Rosetta code reference came out last month (you should be able to figure out which author is me!)

Methods Enzymol. 2011;487:545-74.
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P.

One of the more recent reviews will cover most of the older reviews:
Biochemistry. 2010 Apr 13;49(14):2987-98.
Practically useful: what the Rosetta protein modeling suite can do for you.
Kaufmann KW, Lemmon GH, Deluca SL, Sheehan JH, Meiler J.

[Anonymous]

I am sorry for making my question a little bit confusing .. Actually there is a paper “High resolution Design of a protein Loop” in which they have used Rosetta for designing a loop of 10 residues for some protein .. I want to follow the same approach like the one given in paper .. For ur convenience I am stating here what they did …

1) they searched the pdb for residues that superimpose the loop residues of their protein..
2)they grafted these fragments on the protein using Monte CArlo optimization and gradient based mnimization , finally loop closure on basis of low energy backbone torsion angles , Hbonds and absence of clashes with neighbouring backbone atoms
3) From these simulation they selected 36 low scoring backbone str.
4) Each of the starting str (from those 36 was used to seed 200 independent sequence design and backbone optimization.

I also want to follow the same suite … but here I don’t have any backbone str. of loop to search a sequence as I want to insert longer loops in my protein… For that I have got a library of fragments of varied length from Prof. George Rose Lab, JHU …
Can I use that lib. together with kinematic loop modeling for that as they have mentioned in the documentation that they modeled a 10 residue loop for an 80 amino acid protein … Pls help ..

Today I was going through Pro. Brian’s site and I found ur name in there and the paper that I have mentioned above was published by one of ur group member…

[Anonymous]

I really appreciate your immediate reply to ur queries …. Due to time shortage I would like to go through the previous version of rosetta i.e 2.3.1 since it works well in my system without problems… I will be able to give some report by next week if everything goes well.. If this will work fine then I will definitely work on the newer version…. writing code and checking errors will take a lot of time .. I will ask her to tell me the way she did … then I will get back to u for the newer version .. but still there is a question about the accuracy of the results from that version ….

[Anonymous]

Did you see the reply above from huxz? She’s the first author of the paper. If you want to do it as she did, then you should reply to her above (I’ll let her know to communicate with you further).

If you want to do this in Rosetta3, then be prepared to start writing a fair amount of C++, because (as she said) this protocol wasn’t ported from ++ to Rosetta3.

A) First you’ll need to figure out how you translate your Rose library into Rosetta fragments using the fragments machinery. I don’t know how to do this. I can contact the fragments person to see if he can help if you go this route. This is likely to be the hard part.
Next you’ll need to compose your protocol out of the existing movers (I assume you looked at the Mover part of the Rosetta3 reference). The lower-level movers will work for your purpose (fragment insertion movers, CCD/KIC movers) but the higher-level movers (like loop modeling overall) may not. You might be able to combine your fragment library after step A) with the existing fragments+CCD loop protocol. If you want to try a fragments+KIC protocol (nobody else has written one, because KIC sampling ignores the input conformation unless you tweak the settings) then you’ll need to write one, modeled after the fragments+CCD protocol.
C) If you are writing your own code, there’s no need to separate design from backbone generation, you can just throw design steps into the middle of loop modeling.

I can offer advice and input on and C) but I can’t write the protocol.

[Anonymous]

Thanks for ur reply and sorry for late reply from my side .. I would like to tell you what I want to do as there is some modification in the protocol that is mentioned in the paper .. Here are the steps which I want to follow ..

1) First of all I have found a library of loop fragments of different sizes (till 25 residues) , I want to use this library for my protein to model the loop .. The reason is that my study involves longer loop insertion in my protein .

2)How can I use rosetta in this ??

Also, if I use older version though the newer one is present ,which one will be better in your opinion considering result accuracy and easy way of doing it (compared to using a older version) ??

Pls do comment ..

[Author]

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