Hi Conrad, first you have to convert the mentioned angles to degree. They are represented as rad here. (first 3 values in the translation file) The formula for this would be rad*180/pi. We don't know why, but for the y angle you have to switch the algebraic sign. Simply multiplied by -1. We just did the conversions in Excel. The rotation in PatchDock is in XYZ notation, first rotation, than translation (this would be the order you also have to use by appling the coordinates) Then we just loaded the receptor as well as the ligand, apply the changes you want (e.g. color active sites etc.) save it into a session file and wrote a little chimera command file containing the following: close session open Z:\Sebastian\2013\Liganden\ohne Liganden\PatchDock\2+3\reference.py cofr 0.0,0.0,0.0 cofr fixed turn x -28.32 models 1 turn y -42.12 models 1 turn z 128.78 models 1 move x 33.96 models 1 move y 68.95 models 1 move z 212.57 models 1 now you can just edit the turn and move values, open the command file and Chimera will perform the orientation. Greets Sebastian 2013/2/12 Conrad Huang <conrad@cgl.ucsf.edu>

Hi, Sebastian.

Just out of curiosity, what is your solution? Thanks.

Conrad

On 2/12/2013 6:00 AM, Sebastian Mock wrote:

...

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 <mailto: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/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>

<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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