Site map - MolProbity

You cannot use your browser's back button in MolProbity, and you cannot have multiple windows of the same working session (except for kinemage views, charts, and the like).

Please continue on from here; no damage was done to your session.

Features in italics have not yet been implemented.

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!)

	Site map
Main page About hydrogens Evaluate X-ray Evaluate NMR Fix up structure Work with kins View & download files Lab notebook Feedback & bugs Site map Save session Log out You are using 0% of your 200 Mb of disk space.	You cannot use your browser's back button in MolProbity, and you cannot have multiple windows of the same working session (except for kinemage views, charts, and the like). Please continue on from here; no damage was done to your session. Features in italics have not yet been implemented. 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!)
About MolProbity \| Website for the Richardson Lab \| Using ecloud x-H \| Internal reference 4.2