[Chimera-users] moving to coordinates

[Sebastian Mock]

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 at 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 at cgl.ucsf.edu <mailto:conrad at 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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