Unsolved

In RosettaScript, the mover "RepackMinimize" has attributes "design_partner1" and "design_partner2" to define which partner will be designed, but it does not have attribute like "jumps" or "partners" (just like "DockingProtocol") to let you set the jump in fold tree. It assumes to use jump=1, this is OK for two-chain complex. But it is not OK for more than two chains.

I applied this mover on a 4-chain complex with "minimize_rb=1":
<RepackMinimize name=des1 scorefxn_repack=soft_rep scorefxn_minimize=soft_rep minimize_bb=0 minimize_rb=1/>

But the program halted with errors:

Hi, I am modeling linkers between domains. There are 2 domains connected by 4 linkers. When I run FloppyTail application, domain docking is performed as if there are 5 domains sequentially connected by 4 linkers. Is there a way to define movemap so that rosetta will consider 2 domains out of 5 as one domain, and the other 3 domains, as another, so that there are 2 domains.

Thanks

Here are my flags

-database /rosetta3.4/rosetta_database/
-in:file:s infile.pdb
-in:file:movemap linksfile
-packing:repack_only
-nstruct 30000
-out:output
-out:file:silent linker_model.out

Hi,

I want to know that how can I access the HBondEnergy of residue residue pair of the HBondSet(). I checked that there is a function called hbond.energy(), but don't know how to use that ?? But when I use it for the residue in pdb to store information using :
for residue in range(1,p.total_residue()+1):

for hbond in range (1,p_hb.nhbonds()+1):
hbond = p_hb.hbond(hbond)
donor = hbond.don_res()
acceptor = hbond.acc_res()
if residue == donor or residue == acceptor:
donor_residues.append(donor); acceptor_residues.append(acceptor)

Hello everyone

I run the following command: etc/make_fragments.pl -nohoms -id fragm blabla/protein.fasta

and I obtain fragments files which contain fragments from the original protein.

moreover running the same command without the -nohoms option I obtain the same output.

Does anybody know why?

Thanks in advance

Alfredo