[Chimera-users] How to to do that in chimera?

Krivic, Denis denis.krivic at medunigraz.at
Thu Apr 9 13:06:52 PDT 2020

To whom it may concern,

I have just started working on a project which includes docking and analysis of the results several weeks ago. So figuring out software for docking and the docking procedure itself was one set of problems (solved), and now I could really use your help in order to analyze my data - docking results (output files).

At the moment, I am using Windows 10 (x64), Chimera 1.14, AutoDock Vina 1.1.2 and AutoDock 4.2.6.

So, I have a protein (ion-channel) and several different ligands, for which I want to see how they and if they (at all) may interact with the protein. Therefore I dock the ligand in the two mentioned programs and got different output files. Vina generates a single file with 9 different positions, and 4.2. generates 9 different files for each position.

Now, the first problem I encountered was that in Chimera I can open and analyze only Vina output (single file). How do I open 4.2. output?

The second problem is that I am able (know how) to analyze polar interactions (HBonds). But can I somehow check for hydrophobic or other kind of interactions?

The third thing is that, for example, I have Vina output files for ligand docked in 2 different (but adjacent) places in protein (so 18 positions in total). Is there any chance to merge those files so I can see the energy differences among all of them?

Fourthly, is there any way to merge vina and an other program's output (4.2 or DOCK for example) and see if there are common structures (same one generated by both) and the ones that are not common for the two?

Finally, is there any graphical way of representing the docking poses and see the likeliness of the binding of a certain poses? Or some sort of clustering of poses into more probable binding candidates or something similar?

Thank you in advance,


What kind of docking
What you want to do, meaning achive
Which steps have you carried out
Description of the status, when you get stuck
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