Using Sybyl to visualize results
Another option for visual examination is through Sybyl by putting the poses in a Sybyl Molecular SpreadSheet. The following contributed script builds such a spreadsheet and populates it with the selected poses and Magnet features:
$M4X_MAGNET_ROOT/contrib/sybTbl.sh pkx1_select.cex pkx1_select.out
Wait until you've seen Sybyl start up in non-graphics mode and quit.
Ignore a message that reads
Cannot access tijdelijk*: No such file or directory
This is what you'll see in your window when the script is done (the script starts and quits Sybyl on its own !)
Sybyl> quit yes
The sybTbl script is provided as-is, unsupported ! You have to have a license to the Sybyl software, and will probably have to edit the call to Sybyl, depending on your system setup.
Start Sybyl and read in your protein pdb-file pkxnoH.pdb
If you want a reference compound to find the ATP binding pocket, read in the docked purine ring, bare_purine.pdb
Open the spreadsheet you created above with the sybTbl command, pkx1_select.tbl
Use the spreadsheet features for sorting and selecting poses with certain feature profiles. Look for poses that make sense based on what you know about protein-ligand interactions, in particular for this class of targets. Use different profiles based on the features in the spreadsheet.
You may have noticed that the atomtypes and connectivities for some poses are messed up. This is the result of the different file conversions.
You may have already noticed additional features you are interested in. You can run Magnet again to specify those features. If you want to run Magnet on a cex file that you already extracted with efcex instead of on the whole docking output, you have to set the argument to getid to zero: getid(0), in the final printf statement. Look at the add.sea file for an example on how to add HB donor and acceptor counts for residue number ###:
substitute ### with the residue number you're interested in (note: there are many places where ### occurs in this file: change them all!)
to run this on the selected poses only:
magnet add.sea protein+plptypes.cex pkx1_select.cex > pkx2.out
You can add these features to the table with the contributed sybCol.sh script:
$M4X_MAGNET_ROOT/contrib/sybCol.sh pkx1_select pkx2.out
The sybCol command can also be used to add features from any other file where the first column contains the pose-identifier and the following columns contain relevant information for those poses. There should be a header line in that AddedFeatureFile, because that is where the Sybyl table gets its column names from.
Again, wait until you've seen Sybyl start up in non-graphics mode and quit. This is what you'll see in your window when the script is done (the script starts and quits Sybyl on its own !)
Sybyl> quit yes
The sybCol script is provided as-is, unsupported! You have to have a license to the Sybyl software, and will probably have to edit the call to Sybyl, depending on your system setup.
Inspect the enhanced table in Sybyl and see if you're learning something more.
Tip: there is a Thr in the bindingsite that makes some nice interactions with docked poses selected to also have hydrogenbonds to the hinge domain and to have several aromatic atoms close to where the purine ring of ATP should sit.
Another example of a case where you may want to run a follow-up Magnet run on already selected poses is when you want to calculate Accessible Surface Area (ASA) features. These typically take much longer, so it makes sense to run them on a selected subset. Check out asa.sea for an example. Again, the features can be added to the Sybyl spreadsheet with the sybCol command.