broker domain insertion

[Anonymous]

Hi 

   I am trying to model c terminus of my protein while keeping the majority of N terminus structure fixed. I an using broker domain insertion for this purpose. in the domain_insertion.xml file, I need to provide topology file for my protein. How can I make the topology file?

 

Thank you

Dhiraj

[Anonymous]

Unfortunately, the application which automatically generates a topology file from a PDB (r_pdb2top) is not part of the Rosetta release.

However, here is an example of the topology file for 1QYS 

PAIRING_STATISTICS 1

STRAND_TOPOLOGY  4 35.8 SINGLE_TOP

PAIRSTAT_ENTRY:  7.00   . A 2-21 to 9-14 reg: 23 pleating: 2 1 2 1 2 1 2 1

PAIRSTAT_ENTRY: 11.60   . A 3-51 to 9-45 reg: 54 pleating: 2 1 2 1 2 1 2

PAIRSTAT_ENTRY: 11.20   . A 45-91 to 51-85 reg: 136 pleating: 1 2 1 2 1 2 1

PAIRSTAT_ENTRY:  6.00   . A 76-91 to 82-85 reg: 167 pleating: 2 1 2 1 2 1 2

And here’s one for 1UBQ

PAIRING_STATISTICS 1

STRAND_TOPOLOGY  5 24 SINGLE_TOP

PAIRSTAT_ENTRY:  4.00   . A 2-16 to 6-12 reg: 18 pleating: 1 2 1 2 1

PAIRSTAT_ENTRY:  2.60   . A 22-55 to 22-55 reg: 77 pleating: 1

PAIRSTAT_ENTRY:  1.00   . A 44-49 to 45-48 reg: 93 pleating: 1 2

PAIRSTAT_ENTRY:  5.00   . A 41-71 to 44-68 reg: 112 pleating: 1 2 1 2

PAIRSTAT_ENTRY: 11.40   . P 4-66 to 7-69 reg: 62 pleating: 2 1 2 1

And here’s one for 1VXA (all alpha helical myoglobin)

PAIRING_STATISTICS 1

STRAND_TOPOLOGY  0 0 SINGLE_TOP

 

The number after the PAIRING_STATISTICS is the number of STRAND_TOPOLOGY entries (always 1 in this case).

The first number after the STRAND_TOPOLOGY is the number of PAIRSTAT_ENTRY lines, and the second is the sum of their weights. (The final entry is always SINGLE_TOP in this case)

There’s one PAIRSTAT_ENTRY line for each strand-strand pair. The first entry on the line is the weight (which is the number of paired residues plus 0.2 times the sequence separation of the two strands minus one) , the second is an “is native” indicator (here ‘.’, indicating we generated without native information), The third is A/P, indicating parallel or antiparallel. The next is the definition of the ends of the pairing: “2-21 to 9-14” means the strand pairing starts at residue 2 (which is hydrogen bonded to residue 21) and ends at residue 9 (which is paired with residue 14) All numbers are in Pose/Rosetta numbering (not PDB numbering). The next is a list of  registers (the difference between the first two numbers for parallel, the sum for antiparallel), followed by annotation of bulges, if any, followed by the pleatings (determined by the relative orientations of the Calphas at and around the respective residues.

 

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