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Generate a trajectory between two states (open and closed)

Directly generates a trajectory PDB file readable by PyMol...
This program works with CA-ONLY; it will extract CA from the PDB file.
It used to be pretty slow but was recently dramatically improved by Patrice Koehl, whose version has now just been installed.

Use the following two commands to generate a C-alpha trace with PyMOL:
set cartoon_trace, 1
show cartoon

Then change colors and play the movie...
You can also download the ligand (if any) separately and show it as CPK.

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters)

PDB file of initial state (CA only) Ex: 1ANF

PDB file of final state (CA only) Ex: 1OMP

Number of steps between the two states

Cutoff for the ENM (Angstroms)

If the cRMS between the 2 structures is high (i.e. larger than 5-6 Angstroms), use 100 steps instead of 50.

If there are some poorly linked domains use a higher cutoff (12-15 Angstroms).

Input data formats

  • The job title is just for your own identification, but note that it will show up in the public job queue (but your results will not be public).

  • The coordinate files should be in PDB format, with only a single structure (no multiple models). Only CA atoms are accepted as this stage; the limit is 1000 residues.

    The two files MUST have the same number of (CA) atoms; they can be aligned externally by Profit, but the program will do it internally anyway.

  • The number of states should be less than 200; usually 50 is enough, but it can happen that the algortihm fails to converge if the steps between successive structures are too large, in which case it may be worth trying 100 steps or even 200.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 18:12 March 16, 2007.