[Chimera-users] moving to coordinates

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 7 11:12:56 PST 2013


Hi Sebastian,
Those numbers in the *.txt file are the same as the last column in the *.res file, and apparently are not coordinates but according to the PatchDock help, 
<http://bioinfo3d.cs.tau.ac.il/PatchDock/help.html>
the ligand's "3D transformation: 3 rotational angles and 3 translational parameters."

Chimera can read in and apply a transformation matrix as described here,
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html>

... or apply a transformation described as Euler angles and translation shift via the Transform Coordinates tool (in menu under Tools... Movement):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html>

Clearly what you get from PatchDock is different from the matrix, and not enough information is given to tell how you would convert one to the other. 

Maybe what PatchDock gives would work if you entered it into the Transform Coordinates tool (again not enough information to tell), but you'd have to compare the result with the PDB of complex downloaded from PatchDock to check.  There are different conventions for transformation angles, and the tool might be using a different one than PatchDock.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html>

It would still be some effort on your part to enter values into Transform Coordinates, even if they work "as is."

Anything fancier, including some conversion from how PatchDock describes the transformation into something that Chiemra can read, would require a new tool or new format reader, or at least a script.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 7, 2013, at 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/docking.res
> 
> Thanks in advance
> Sebastian



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