Tutorials: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary Tag: Manual revert |
||
| (108 intermediate revisions by 5 users not shown) | |||
| Line 1: | Line 1: | ||
== Downloads == | == Downloads == | ||
* Latest [[Media:cyana-3. | * Latest [[Media:cyana-3.98.15bin-240809Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (09.08.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations. | ||
* [ | * On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs. | ||
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB). | |||
== INCLAN Tutorials == | == INCLAN Tutorials == | ||
| Line 10: | Line 11: | ||
* [[Using INCLAN control statements]] | * [[Using INCLAN control statements]] | ||
== | == CYANA Tutorials == | ||
* [[Defining non-standard residues]] | |||
<!-- | |||
* [[eNORA and multi-state structure calculations]] | |||
--> | |||
== CYANA example calculations == | |||
* [[Basic structure calculation starting from given restraints]] | * [[Basic structure calculation starting from given restraints]] | ||
| Line 16: | Line 24: | ||
* [[Structure calculation with automated NOESY assignment]] | * [[Structure calculation with automated NOESY assignment]] | ||
* [[Homodimer structure calculation with automated NOESY assignment]] | * [[Homodimer structure calculation with automated NOESY assignment]] | ||
* [[ENORA and multi-state structure calculations]] | |||
* [[Identification of key NOEs]] | |||
* [[Determination of the protein state populations]] | |||
* [[Determination of the protein number of states]] | |||
* [[Peaklist preparation for eNOE pipeline]] | |||
<!-- | |||
* [[Structure calculations using residual dipolar coupling restraints]] | * [[Structure calculations using residual dipolar coupling restraints]] | ||
* [[Structure calculations using pseudocontact shift restraints]] | * [[Structure calculations using pseudocontact shift restraints]] | ||
| Line 35: | Line 49: | ||
** [[Calculate RMSD values and mean structures]] | ** [[Calculate RMSD values and mean structures]] | ||
** [[Angle restraints from the program TALOS]] | ** [[Angle restraints from the program TALOS]] | ||
--> | |||
== Courses == | |||
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR === | |||
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage]) | |||
<!-- | |||
=== Biomolecular NMR: Advanced tools PhD course === | |||
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage]) | |||
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]] | |||
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]] | |||
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 === | |||
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage]) | |||
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]] | |||
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]] | |||
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]] | |||
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017) | |||
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015) | |||
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014) | |||
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013) | |||
--> | |||
== Input file formats == | == Input file formats == | ||
Latest revision as of 10:34, 20 September 2024
Downloads
- Latest demo version of CYANA 3.98.15 for Linux and MacOS (09.08.2024)
The demo version has the full functionality of the program for the protein sequences that are used in the example calculations. - On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.
- Results of all CYANA 3.98.13 demo calculations (93 MB).
INCLAN Tutorials
CYANA Tutorials
CYANA example calculations
- Basic structure calculation starting from given restraints
- Structure calculation using manually assigned NOESY peak lists
- Structure calculation with automated NOESY assignment
- Homodimer structure calculation with automated NOESY assignment
- ENORA and multi-state structure calculations
- Identification of key NOEs
- Determination of the protein state populations
- Determination of the protein number of states
- Peaklist preparation for eNOE pipeline
Courses
EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR
Grenoble, 30 August – 6 September 2024 (course homepage)
Input file formats
- Residue library file (.lib)
- Sequence file (.seq)
- Distance restraint file (.upl, .lol)
- Torsion angle restraint file (.aco)
- Residual dipolar coupling restraint file (.rdc)
- Pseudocontact shift restraint file (.pcs)
- DG Cartesian coordinate file (.cor)
- PDB coordinate file (.pdb)
- Torsion angle file (.ang)
- XEASY chemical shift list file (.prot)
- BMRB chemical shift list file (.bmrb)
- XEASY peak list file (.peaks)
- NMRView peak list file (.xpk)