I know firsthand that Rosetta works even for proteins >200 residues,
meaning it will make them much better in terms of energy and
stereochemistry. Now, if you are expecting that the program will remove
absolutely all problems with the model so it gets a perfect Molprobity
score, that would be unrealistic. It seems to me that you already have a
pretty good model - it doesn't have to be free of all violations to be
useful. Even many legitimate protein structures, which are based on
experimental maps, have "issues" when analyzed by Molprobity.
Having said all of this, I have good experience with RAPPER when it comes
to loop modeling, assuming loops are of reasonable length. The program is here:
If you get the program to install and work properly, I can offer you a
small script that will take a PDB file and a range of residues for
refinement, and produce a new model resampled loops. Alternatively, you can
send me your PDB file and a range of residues to be refined and I will send
you the model back. If you are happy with it, then you can spend more time
installing and optimizing RAPPER.
Good luck,
Mensur
At 06:24 PM 1/5/2011, Irene Newhouse wrote:
I'm a relatively new user of modeller & successfully built a fairly nice
model of a protein with 258 residues. It forms a homodimer, and has to be
modeled as a dimer, because there's a very flexible loop that can easily
adopt conformation that prevent dimerization if the 2nd unit isn't
present. [I confirmed that by trying it].
Someone on this group suggested the Molprobity server as a way to assess
model quality, for which I'm very grateful. He also suggested relaxing the
structure with Rosetta, & after epic battles with python setup & my
operating system, I got it up & running. Only to learn from the
RosettaCommons forum that Rosetta relax doesn't scale well with chain
length & isn't useful for proteins with >200 residues. I managed to get
the Molprobity score down to a respectable 2.-something using lots & lots
of iterations of Schrodinger Prime loop refinement & side chain
minimization. It took about a week of setting up a loop, running it,
checking to see if it refined, iterating 'til I could move on, etc. So I'm
looking for something a bit less hands-on, if possible. Also, Schrodinger
is expensive & my boss may not renew the licenses when this lot expires in
March. And finally, Molprobity signaled several C-beta issues in my
structure, & Schrodinger just doesn't seem to do much about
those. Therefore, I'm looking for other suggestions, preferably freeware,
for model refinement. I have tried some loop refinement with Modeller
itself, but wasn't thrilled with the outcome. This could easily be because
I couldn't find sample scripts to copy, or an explanation of how to tweak
the parameters if the loop doesn't seem to be refining. If anyone can
point me in those directions, I'd be grateful, too.