6
edits
Crystallography: Difference between revisions
Jump to navigation
Jump to search
→Software Packages
Biophysics (talk | contribs) (→Software Packages: add ccp4mg) |
|||
| (19 intermediate revisions by 4 users not shown) | |||
| Line 4: | Line 4: | ||
* [[Twinning]] | * [[Twinning]] | ||
* [[R-factors]] | * [[R-factors]] | ||
* [[Bulk solvent correction]] | |||
* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction] | * [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction] | ||
* [[Disorder]] | |||
* [[References and links]] | * [[References and links]] | ||
== Procedures == | |||
* [[Solve-TAT|Solving a structure]] | |||
* [[Solve a small-molecule structure]] | |||
* [[Buildn-TAT|Model building and refinement]] | |||
* [[Evaluation-TAT|Model Evaluation and Interpretation]] | |||
== Crystallography Software == | == Crystallography Software == | ||
| Line 20: | Line 28: | ||
* [[Model validation]] | * [[Model validation]] | ||
* [[Model Evaluation]] | * [[Model Evaluation]] | ||
* [[Loop modelling]] | |||
=== Automated Pipelines for Structure Solution === | === Automated Pipelines for Structure Solution === | ||
*[[Ants]] | *[[Ants]] | ||
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] | *[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] | ||
*[ | *[https://www.globalphasing.com/sharp/ autoSHARP] | ||
*[[BALBES]] | *[[BALBES]] | ||
*[[BNP]] | *[[BNP]] | ||
| Line 34: | Line 43: | ||
=== Web services === | === Web services === | ||
*[http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)] | * [http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)] | ||
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]] | * [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]] | ||
*[http://tuna.tamu.edu/ Bias removal server] | * [http://tuna.tamu.edu/ Bias removal server] | ||
*[ | * York suite (Balbes, Modsearch, [https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html Zanuda]) | ||
*[http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server] | * [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server] | ||
* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections] | |||
* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [http://dx.doi.org/10.1073/pnas.1012095107]. | |||
* [http://witold.med.virginia.edu/fitmunk/server/ Fitmunk] takes a PDB and MTZ file, and helps to identify your protein by electron density based sequencing, and by fitting different conformations. See https://www.ncbi.nlm.nih.gov/pubmed/26894674 and https://www.ncbi.nlm.nih.gov/pubmed/26660914 | |||
* [https://staraniso.globalphasing.org/ STARANISO] analyses, corrects and visualises diffraction data for data anisotropy; see also [https://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi PDBpeep] for deposited PDB entries. | |||
* [http://grade.globalphasing.org/ Grade] to create restraint dictionaries for refinement | |||
=== Software Packages === | === Software Packages === | ||
| Line 56: | Line 70: | ||
* [[SHARP]] [http://www.globalphasing.com homepage] | * [[SHARP]] [http://www.globalphasing.com homepage] | ||
* [http://www.solve.lanl.gov/index.html Solve/Resolve] | * [http://www.solve.lanl.gov/index.html Solve/Resolve] | ||
* ... | * [http://rna.ucsc.edu/pdbrestraints/ PDB coordinates to Restraints] - This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted. | ||
* [https://www.globalphasing.com/ Global Phasing Ltd] (data processing, structure solution, refinement - BUSTER, SHARP/autoSHARP, autoPROC, Grade, Rhofit, Pipedream, STARANISO) | |||
=== Libraries for crystallography and related areas === | === Libraries for crystallography and related areas === | ||
| Line 64: | Line 79: | ||
* [[mmdb]] | * [[mmdb]] | ||
=== Tricks | === Tips and Tricks === | ||
* [[Finding symmetry elements in P1]] | * [[Finding symmetry elements in P1]] | ||
* [[Programs to convert X-ray diffraction image file formats to graphics file formats]] | |||
== Teaching crystallography == | == Teaching crystallography == | ||
=== [[Crystallography courses on the web]] === | |||
=== [[Crystallography books]] === | |||
=== [[Test data sets]] === | |||
=== The effect of resolution on electron density === | |||
* James Holton's movie [[https://bl831.als.lbl.gov/~jamesh/movies/resolution.mpeg]] | |||
== Understanding and extending the properties and limitations of crystallographic computations == | == Understanding and extending the properties and limitations of crystallographic computations == | ||