• Home
• Introduction
  • What is PONDEROSA-C/S?
  • What makes it so innovative?
  • Side-by-side comparisons
• Programs
  • Ponderosa Client
  • Ponderosa Server
  • Ponderosa Analyzer
  • Ponderosa Violation Investigator
  • Download
• Examples
  • An example set for demonstration
  • For Users
  • For Administrators
• Contact
  • User Group
  • Email Contact
• Screen Shots
• Video Tutorials
• Web Servers
  • PONDEROSA-C/S Web Server
  • PONDEROSA Prediction Server
• NMRFAM
  • ADAPT-NMR
  • ADAPT-NMR Enhancer
  • ARECA
  • I-PINE Web Server
  • LACS
  • NEWTON
  • PACSY
  • PACSY-ALIGN
  • PONDEROSA
  • PINE-SPARKY
  • PINE-SPARKY.2
  • RNA-PAIRS
  • rNMR
  • RUNER Web Server
  • NMRFAM-SPARKY
  • Software Downloads

  Welcome to NMRFAM Ponderosa Web Server.

Please upload your packed_inputs.txt file from Ponderosa Client working directory.
In other way, you can use two-letter-code "c3" in NMRFAM-SPARKY for quick submission.
Your result will be back in a few minutes to hours depending on your settings.

Currently, NMRFAM Ponderosa Web Server accepts:
1) Any academic projects with 7 different options,
2) Collaborative projects with 10 different options.

[Click here to download Ponderosa Client program for input preparation]

	Any academic users	Collaborators
CPU	20	40
Tiers	1	2
Steps	4	5
Supported Calculation Engines	1. AUDANA/AUDASA automation 2. (ss)PONDEROSA-X refinement 3. Constraints only-X (40 sampling) 4. Constraints only-X for final step (Implicit Water Refinement/100 sampling) 5. Constraints only-X for final step (Explicit Water Refinement/100 sampling) 6. Constraints only-X for final step (x2) (Implicit Water Refinement/200 sampling) 7. Constraints only-X for final step (x2) (Explicit Water Refinement/200 sampling)	* Additional options: 8. CYANA calculation 9. PONDEROSA refinement 10. Constraints only

1. Keep file name as packed_inputs.txt !!!
2. Set User Name and Key Phrase as guest if you are not NMRFAM collaborator.
[Constraints Only-X(2)], [PONDEROSA-X refinement]

User Name (or guest): 
Key Phrase (or guest):
packed_inputs.txt:

Use PACSY DB for better NOE assignment (recommended)
PDB ID: , CHAIN ID: 
Do not use any information from same sequence proteins

Type select PDB_ID,CHAIN_ID from PDBSEQ_DB in PACSY web server to check template coverage.
Check PACSY-ALIGN to user defined coordinate file to enhance automated NOE assignments.

* Check your running jobs here.
Your E-mail: Check

Please review chemical shift assignment quality results from ARECA.
You will receive ARECA results right after submitting a job.