Clash Score and Quality Analysis at MolProbity
Provided as part of FirstGlance in Jmol.
The server is straightforward but has many options. This will guide you through the steps to get the clash score and additional quality analysis.

1. Go to the MolProbity Server.


2. At the Main Page, enter your PDB code into the slot at the top and click the button Fetch (or upload your model).


3. A list of characteristics of the model will appear. Click Continue. You will arrive back at the Main Page. Click the link to add hydrogens.


4. At the Add Hydrogens page, simply click the button at the bottom Start Adding H.


5. At the Review Flips page, MolProbity recommends whether to flip certain Gln, Asn, or His sidechains. You can uncheck the flips if you wish. Then click the button Regenerate H, applying only selected flips. (Or if no flips were recommended, click Continue.)


6. At the page Added H with -build you have the option to view sidechains of Gln, Asn and His in both 180 degree orientations (original and flipped), showing clashes and energetically favorable interactions.
   
   Click the button Continue.


7. You are returned to the Main Page. Click the link Analyze all-atom contacts and geometry.


8. At the page Analyze all-atom contacts and geometry, you can leave all the default options as they are, or change them. Then click the button Run programs to perform these analyses.


9. Now you have your results at the page Analysis output. The results are colored  green  for good,  yellow  for not so good, and  red  for worrisome, according to their values for your particular model. In particular, note the Clashscore and MolProbity score.

Now you are finished with the basic quantitative analysis.

While still on the Analysis output page, note the options to view clashes and other results in 3D: Multi-criterion KineMage: View in KiNG. (KiNG is a java applet: KineMage New Generation.)

Clashes can be viewed in Jmol in Jmol's Validation Visualization tool.