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Please cite the following:

Haddadian, E. J., Gong H., Jha A. K., Yang X., DeBartolo J., Hinshaw J. R., Rice P. A., Sosnick T. R., Freed K. F. 2011. Automated real-space refinement of protein crystal structures using a realistic backbone move set. Biophysical Journal 101: 899-909

STEP 1: INPUT STRUCTURES

Upload initial Structure A in PDB format:

Upload final Structure B:




STEP 2: CONFIGURE STAGE 1 MORPHING

Enter chain ID and the range of residues (by index number) to undergo dihedral angle moves (e.g. "A,22,33" = move residues 22-33 on Chain A, put each range on a separate line, and use chain ID = A if none exists):

Enter chain ID and range of residues (by index number) whose final positions should match reference structure (enter same as above, but not yet fully implemented):

Choose movetype: φ,ψ noise level (in degrees) =

STEP 3: CONFIGURE STAGE 2 MORPHING

Enter chain ID and the range of residues to undergo dihedral angle moves :

Enter chain ID and range of residues whose final positions should match reference structure (not fully implemented):

Choose movetype: φ,ψ noise level (in degrees) =

STEP 4: Enter your email address here






Only change the following parameters if you are an advanced user

Stage 1 Parameters and Energy Terms:

Reference similarity: Tors Stat Pot (w/NN effects): Tors Stat Pot: Steric overlap: Hbond: DOPE-PW: DOPE-PW Energy terms (leave alone if unfamiliar) EE (local): HH (local): CC (local): EE (antiparallel): EE (parallel): 0A: 1A: 2A:
Seed Input:

Sample ω angle: noise level (in degrees) =

Pathway of PDB files: Save structures every (0.1 Å minimum) change in RMSD

Stage 2 Parameters and Energy Terms:

Reference similarity: Tors Stat Pot (w/NN effects): Tors Stat Pot: Steric overlap: Hbond: DOPE-PW: DOPE-PW Energy EE (local): HH (local): CC (local): EE (antiparallel): EE (parallel): 0A: 1A: 2A:

Seed Input:

Sample ω angle: noise level (in degrees) =

Save structures every (0.1 Å min)


Simulated Annealing terms

MAX TEMP INIT STEPS: MAX TEMP ACCEPT RATIO: TEMP UPDATE INTERVAL: DEFAULT INIT TEMP: SMOOTH DEVIATION COEFFICIENT: UPDATE TEMP COEFFICIENT: TEMP CONVERGENCE COEFFICIENT:
CALCULATE INIT TEMP: CHECK TEMP CONVERGENCE: LOCAL MINIMIZATION: