[chimerax-users] Analysis of the protein-ligand interactions using ViewDock

[Elaine Meng]

Hello,
You will need to actually try the steps yourself to work out the protocol, but I can give you a few pointers.  First (before trying to write a script) you should just use trial and error of typing commands directly into the command line yourself to figure out what they should be.

(1) of course you can open the receptor PDB, command "open"
...for local file
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>
...or fetch from PDB
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>

(2) I don't know what format your docked ligands are in.  ChimeraX tool ViewDockX knows some but not all of the same formats that Chimera knows.   Since what you describe is showing all of the docked ligands together at the same time, it may not be necessary to use the ViewDockX tool.  If you don't use it, however, you would still need to use some format that ChimeraX knows how to read.
You would use the "open" command if it is a file that ChimeraX can read.  If not, you would have to keep using Chimera.

ViewDockX formats
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

atomic structure formats known to ChimeraX in general
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>

(3) then if you can actually open the docked ligands, you can see in the Model Panel (when you are trying this interactively) what their model number(s) are, to later use in commands in your script. If you are using a command to find hbonds, you don't need to select the ligands, however -- you can specify them directly in the hbonds command.

(4)  ChimeraX and Chimera both have commands to find H-bonds.  In ChimeraX the command is "hbonds" and you can specify the docked ligand model(s) directly, e.g.  if they are all in #2, "hbonds #2 restrict any reveal true saveFile myoutputfile.txt" -- but please read the help to see what options you want:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html>

Another way in ChimeraX to figure out the hbonds command is to use the H-Bonds graphical interface: menu: Tools... Structure Analysis... H-Bonds.  Then when you click OK or Apply, the corresponding command will be shown in the Log.  One difference, however, is that if using the GUI you would need to select the ligands first (which can be done with the Model panel checkboxes under the selecting-hand icon, or command like "select #2") whereas the "hbonds" command allows simply specifying them in the command, as in my example command above.

I cannot overemphasize, however, that you should not expect to write a script, or have somebody just give you a script and have the whole thing work right away -- most experts can't even do that, including me -- instead you really need to try the commands interactively on your specific data and see what works before putting them in a script.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 4, 2022, at 8:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users!
> 
> I would like to use ChimeraX to calculate protein-ligand contacts
> established in docking calculations for the ensemble of the docking
> solutions (88 conformations of the ligand saved in multi-model
> format). Basically using the GUI of the UCSF Chimera previously I
> could do the following routine for the analysis of docking results:
> 1. Open the protein PDB
> 2. Use the Surface/Binding Analysis > ViewDock tool to open the docking poses
> 3. Using the Model Panel, select all docking poses
> 4. Use the Surface/Binding Analysis >  FindHBond tool to locate all
> H-bonds. Make sure to check "Only find H-bonds with at least 1 end
> selected". You can check "write information to file" to save the
> H-bonds.
> 
> May I adapt this protocol with the ChimeraX to perform such computing
> in batch (no-gui mode)? What should be the differences in the commands
> between Chimera and ChimeraX ( I've already seen that ViewDock is
> available in the ChimeraX as well...)
> Many thanks in advance!
> Cheers
> Enrico
> _