Site map

Input files

• Upload PDB files from local disk.
• Retrieve PDB files from the PDB or NDB.
• Upload kinemages for viewing in KiNG.
• Upload electron density maps.
• Retrieve 2Fo-Fc and Fo-Fc (difference) maps from the EDS.
• Upload custom heterogen dictionaries (for adding hydrogens).

Edit PDB files

• Remove unwanted chains.
• Specify crystallographic resolution.

Downgrade PDB to v2.3

• Downgrade an uploaded PDB to v2.3 (for download only)

Add hydrogens

• Add missing hydrogens.
• Optimize H-bond networks.
• Check for Asn, Gln, His flips.

Analyze all-atom contacts and geometry

• All-atom steric contacts (clashlist, clash score, contact dots)
• Protein geometry evaluation (Ramachandran plot, rotamers, Cβ deviations)
• Nucleic acid geometry (base-phosphate perpendiculars, suite names)
• Evaulate protein and nucleic acid bond lengths and angles
• Multi-criterion chart and kinemage displays

Visualize interface contacts

• Offers detailed control over running Probe to visualize steric interactions.
• Displaying contacts between two subunits or chains is common, but other uses are possible.

Refit sidechains

• ALPHA TEST - not for general public use.
• Automatically refit sidechains based on electron density and all-atom contacts.

Make simple kinemages

• Make kinemages using basic Prekin scripts.
• Kinemages can be combined and edited in KiNG with File | Append.
• KiNG can save modified kinemages to the server with File | Save as.

Fill protein gaps

• ALPHA TEST - not for general public use.
• Fill gaps in protein structures automatically.

Analyze all-atom contacts and geometry for ensembles

• Multi-criterion kinemage for multi-model ensembles

View & download files

• View the original files you submitted or retrieved from the network.
• View kinemages, charts, and other files created by MolProbity.
• Download all files packaged as a ZIP, or individual files one at a time.

Lab notebook

• See notebook entries made automatically by MolProbity.
• Annotate automatic entries with notes and comments.
• Create your own new entries in the notebook.
• Print the notebook or save it as an HTML page.

Feedback & bugs

• Report problems with MolProbity or suggestions for improvement.

Save session

• Save your results from this session and come back later to keep working.
• Creates a page that can be bookmarked in your web browser.

Log out

• Destroy all the files created during this session.
• Start over with a new session, if you want.
• Free up disk space for other users. (Thanks!)