Hi again, we figured it out by ourselves. No need to investigate this further! Thanks anyway! :-) Sebastian 2013/2/11 Conrad Huang <conrad@cgl.ucsf.edu>

Can you please send me the receptor and ligand PDB files as well? Perhaps we can cobble together something.

Conrad

On 2/7/13 1:13 AM, Sebastian Mock wrote:

...

Hi,

I am using Patchdock Algorithm to dock two Enzymes.

I get the pdb's and can load them into Chimera without having problems.

Because Patchdock only performs a jigsaw puzzle with the two molecules, I have to look at all the solutions it gave me and judge them by some criteria. This is very time consuming, as I have to match every single solution with the appropriate molecules in chimera and I get tons of solutions. I found the following two lists with imo coordinates of the dockings. Is it possible to load these into Chimera or at least to enter the coordinates, so that chimera moves the docking partner and I can just look at it and discard or accept?

These are the example lists http://bioinfo3d.cs.tau.ac.il/**PatchDock/runs/1_Hexokinase_** combined.pdb_2_G6PIsomerase_**combined.pdb_37_58_16_6_1_113/**trans.txt<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6PIsomerase_combined.pdb_37_58_16_6_1_113/trans.txt> http://bioinfo3d.cs.tau.ac.il/**PatchDock/runs/1_Hexokinase_** combined.pdb_2_G6PIsomerase_**combined.pdb_37_58_16_6_1_113/**docking.res<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6PIsomerase_combined.pdb_37_58_16_6_1_113/docking.res>

Thanks in advance Sebastian

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