https://wiki.uni-konstanz.de/ccp4/api.php?action=feedcontributions&user=ClemensVonrhein&feedformat=atomCCP4 wiki - User contributions [en]2024-03-29T05:28:23ZUser contributionsMediaWiki 1.39.6https://wiki.uni-konstanz.de/ccp4/index.php?title=Crystallography&diff=2771Crystallography2021-04-23T13:57:03Z<p>ClemensVonrhein: /* Software Packages */</p>
<hr />
<div>== Crystallographic Theory ==<br />
* [[Basics of Crystallography]]<br />
* [[Phase problem]], and [[Phasing]]<br />
* [[Twinning]]<br />
* [[R-factors]]<br />
* [[Bulk solvent correction]]<br />
* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction]<br />
* [[Disorder]]<br />
* [[References and links]]<br />
<br />
== Procedures ==<br />
* [[Solve-TAT|Solving a structure]]<br />
* [[Solve a small-molecule structure]]<br />
* [[Buildn-TAT|Model building and refinement]]<br />
* [[Evaluation-TAT|Model Evaluation and Interpretation]]<br />
<br />
== Crystallography Software ==<br />
<br />
=== For Specific Tasks ===<br />
* [[Data reduction]]<br />
* [[Molecular replacement]] (MR)<br />
* [[Substructure determination]] <br />
* [[Experimental phasing]] (SIR/MIR and SAD/MAD)<br />
* [[Electron density modification]] <br />
* [[Automated Model building]]<br />
* [[Interactive Model building]]<br />
* [[Refinement]]<br />
* [[Model validation]]<br />
* [[Model Evaluation]]<br />
* [[Loop modelling]]<br />
<br />
=== Automated Pipelines for Structure Solution ===<br />
*[[Ants]]<br />
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]<br />
*[https://www.globalphasing.com/sharp/ autoSHARP]<br />
*[[BALBES]]<br />
*[[BNP]]<br />
*[[CRANK]]<br />
*[[Elves]]<br />
*[[MrBUMP]] - molecular replacement<br />
*[[Phenix]] - comprehensive package<br />
*[[HKL2MAP]] - SAD/MAD/SIRAS/SIR phasing based on [[SHELXC/D/E]]<br />
<br />
=== Web services ===<br />
* [http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]<br />
* [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]<br />
* [http://tuna.tamu.edu/ Bias removal server]<br />
* York suite (Balbes, Modsearch, [https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html Zanuda])<br />
* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]<br />
* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]<br />
* [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].<br />
* [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<br />
* [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.<br />
* [http://grade.globalphasing.org/ Grade] to create restraint dictionaries for refinement<br />
<br />
=== Software Packages ===<br />
(large packages first)<br />
* [[CCP4]]<br />
* [[CNS]]<br />
* [[PHENIX]]<br />
* [[SHELX C/D/E]] and [[SHELXL]] (homepage at [http://shelx.uni-ac.gwdg.de/SHELX], [http://dx.doi.org/10.1107/S0108767307043930 overview paper])<br />
* moleman, lsqman, ... from [http://xray.bmc.uu.se/usf/ Uppsala Software Factory]<br />
* XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds homepage] and [http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS XDSwiki]<br />
* HKL [http://www.hkl-xray.com homepage]<br />
* [[COOT]]<br />
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki<br />
* [[CCP4mg]]<br />
* [[O]]<br />
* [[ARP/wARP]]<br />
* [[SHARP]] [http://www.globalphasing.com homepage]<br />
* [http://www.solve.lanl.gov/index.html Solve/Resolve]<br />
* [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.<br />
* [https://www.globalphasing.com/ Global Phasing Ltd] (data processing, structure solution, refinement - BUSTER, SHARP/autoSHARP, autoPROC, Grade, Rhofit, Pipedream, STARANISO)<br />
<br />
=== Libraries for crystallography and related areas ===<br />
* [[Clipper]]<br />
* [[cctbx|Crystallographic Toolbox]]<br />
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html]<br />
* [[mmdb]]<br />
<br />
=== Tips and Tricks ===<br />
* [[Finding symmetry elements in P1]]<br />
* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]<br />
<br />
== Teaching crystallography ==<br />
=== [[Crystallography courses on the web]] ===<br />
=== [[Crystallography books]] ===<br />
=== [[Test data sets]] ===<br />
=== The effect of resolution on electron density ===<br />
* James Holton's movie [[https://bl831.als.lbl.gov/~jamesh/movies/resolution.mpeg]]<br />
<br />
== Understanding and extending the properties and limitations of crystallographic computations ==<br />
<br />
=== Ensemble refinement, and molecular dynamics ===<br />
# Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [http://dx.DOI.org/10.1126/science.271.5245.72]<br />
# Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [http://dx.doi.org/10.1016/j.str.2004.02.031]<br />
# Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [http://dx.doi.org/10.1016/j.str.2007.06.019] <br />
# A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [http://dx.doi.org/10.1038/nsb0397-202] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)<br />
<br />
=== Electron microscopy and X-ray ===<br />
# Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [http://dx.doi.org/10.1016/S0969-2126(99)80120-8]<br />
<br />
=== NMR versus X-ray ===<br />
A couple of papers analysing and comparing NMR and X-ray methods/structures:<br />
# Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [http://dx.doi.org/10.1126/science.1502561]<br />
# X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website.<br />
# Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. [http://dx.doi.org/10.1371/journal.pcbi.0020009]</div>ClemensVonrheinhttps://wiki.uni-konstanz.de/ccp4/index.php?title=Crystallography&diff=2770Crystallography2021-04-23T13:55:06Z<p>ClemensVonrhein: /* Web services */</p>
<hr />
<div>== Crystallographic Theory ==<br />
* [[Basics of Crystallography]]<br />
* [[Phase problem]], and [[Phasing]]<br />
* [[Twinning]]<br />
* [[R-factors]]<br />
* [[Bulk solvent correction]]<br />
* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction]<br />
* [[Disorder]]<br />
* [[References and links]]<br />
<br />
== Procedures ==<br />
* [[Solve-TAT|Solving a structure]]<br />
* [[Solve a small-molecule structure]]<br />
* [[Buildn-TAT|Model building and refinement]]<br />
* [[Evaluation-TAT|Model Evaluation and Interpretation]]<br />
<br />
== Crystallography Software ==<br />
<br />
=== For Specific Tasks ===<br />
* [[Data reduction]]<br />
* [[Molecular replacement]] (MR)<br />
* [[Substructure determination]] <br />
* [[Experimental phasing]] (SIR/MIR and SAD/MAD)<br />
* [[Electron density modification]] <br />
* [[Automated Model building]]<br />
* [[Interactive Model building]]<br />
* [[Refinement]]<br />
* [[Model validation]]<br />
* [[Model Evaluation]]<br />
* [[Loop modelling]]<br />
<br />
=== Automated Pipelines for Structure Solution ===<br />
*[[Ants]]<br />
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]<br />
*[https://www.globalphasing.com/sharp/ autoSHARP]<br />
*[[BALBES]]<br />
*[[BNP]]<br />
*[[CRANK]]<br />
*[[Elves]]<br />
*[[MrBUMP]] - molecular replacement<br />
*[[Phenix]] - comprehensive package<br />
*[[HKL2MAP]] - SAD/MAD/SIRAS/SIR phasing based on [[SHELXC/D/E]]<br />
<br />
=== Web services ===<br />
* [http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]<br />
* [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]<br />
* [http://tuna.tamu.edu/ Bias removal server]<br />
* York suite (Balbes, Modsearch, [https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html Zanuda])<br />
* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]<br />
* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]<br />
* [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].<br />
* [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<br />
* [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.<br />
* [http://grade.globalphasing.org/ Grade] to create restraint dictionaries for refinement<br />
<br />
=== Software Packages ===<br />
(large packages first)<br />
* [[CCP4]]<br />
* [[CNS]]<br />
* [[PHENIX]]<br />
* [[SHELX C/D/E]] and [[SHELXL]] (homepage at [http://shelx.uni-ac.gwdg.de/SHELX], [http://dx.doi.org/10.1107/S0108767307043930 overview paper])<br />
* moleman, lsqman, ... from [http://xray.bmc.uu.se/usf/ Uppsala Software Factory]<br />
* XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds homepage] and [http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS XDSwiki]<br />
* HKL [http://www.hkl-xray.com homepage]<br />
* [[COOT]]<br />
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki<br />
* [[CCP4mg]]<br />
* [[O]]<br />
* [[ARP/wARP]]<br />
* [[SHARP]] [http://www.globalphasing.com homepage]<br />
* [http://www.solve.lanl.gov/index.html Solve/Resolve]<br />
* [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.<br />
<br />
=== Libraries for crystallography and related areas ===<br />
* [[Clipper]]<br />
* [[cctbx|Crystallographic Toolbox]]<br />
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html]<br />
* [[mmdb]]<br />
<br />
=== Tips and Tricks ===<br />
* [[Finding symmetry elements in P1]]<br />
* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]<br />
<br />
== Teaching crystallography ==<br />
=== [[Crystallography courses on the web]] ===<br />
=== [[Crystallography books]] ===<br />
=== [[Test data sets]] ===<br />
=== The effect of resolution on electron density ===<br />
* James Holton's movie [[https://bl831.als.lbl.gov/~jamesh/movies/resolution.mpeg]]<br />
<br />
== Understanding and extending the properties and limitations of crystallographic computations ==<br />
<br />
=== Ensemble refinement, and molecular dynamics ===<br />
# Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [http://dx.DOI.org/10.1126/science.271.5245.72]<br />
# Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [http://dx.doi.org/10.1016/j.str.2004.02.031]<br />
# Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [http://dx.doi.org/10.1016/j.str.2007.06.019] <br />
# A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [http://dx.doi.org/10.1038/nsb0397-202] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)<br />
<br />
=== Electron microscopy and X-ray ===<br />
# Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [http://dx.doi.org/10.1016/S0969-2126(99)80120-8]<br />
<br />
=== NMR versus X-ray ===<br />
A couple of papers analysing and comparing NMR and X-ray methods/structures:<br />
# Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [http://dx.doi.org/10.1126/science.1502561]<br />
# X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website.<br />
# Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. [http://dx.doi.org/10.1371/journal.pcbi.0020009]</div>ClemensVonrheinhttps://wiki.uni-konstanz.de/ccp4/index.php?title=Crystallography&diff=2769Crystallography2021-04-23T13:32:02Z<p>ClemensVonrhein: /* Automated Pipelines for Structure Solution */</p>
<hr />
<div>== Crystallographic Theory ==<br />
* [[Basics of Crystallography]]<br />
* [[Phase problem]], and [[Phasing]]<br />
* [[Twinning]]<br />
* [[R-factors]]<br />
* [[Bulk solvent correction]]<br />
* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction]<br />
* [[Disorder]]<br />
* [[References and links]]<br />
<br />
== Procedures ==<br />
* [[Solve-TAT|Solving a structure]]<br />
* [[Solve a small-molecule structure]]<br />
* [[Buildn-TAT|Model building and refinement]]<br />
* [[Evaluation-TAT|Model Evaluation and Interpretation]]<br />
<br />
== Crystallography Software ==<br />
<br />
=== For Specific Tasks ===<br />
* [[Data reduction]]<br />
* [[Molecular replacement]] (MR)<br />
* [[Substructure determination]] <br />
* [[Experimental phasing]] (SIR/MIR and SAD/MAD)<br />
* [[Electron density modification]] <br />
* [[Automated Model building]]<br />
* [[Interactive Model building]]<br />
* [[Refinement]]<br />
* [[Model validation]]<br />
* [[Model Evaluation]]<br />
* [[Loop modelling]]<br />
<br />
=== Automated Pipelines for Structure Solution ===<br />
*[[Ants]]<br />
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]<br />
*[https://www.globalphasing.com/sharp/ autoSHARP]<br />
*[[BALBES]]<br />
*[[BNP]]<br />
*[[CRANK]]<br />
*[[Elves]]<br />
*[[MrBUMP]] - molecular replacement<br />
*[[Phenix]] - comprehensive package<br />
*[[HKL2MAP]] - SAD/MAD/SIRAS/SIR phasing based on [[SHELXC/D/E]]<br />
<br />
=== Web services ===<br />
* [http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]<br />
* [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]<br />
* [http://tuna.tamu.edu/ Bias removal server]<br />
* York suite (Balbes, Modsearch, [https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html Zanuda])<br />
* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]<br />
* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]<br />
* [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].<br />
* [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<br />
<br />
=== Software Packages ===<br />
(large packages first)<br />
* [[CCP4]]<br />
* [[CNS]]<br />
* [[PHENIX]]<br />
* [[SHELX C/D/E]] and [[SHELXL]] (homepage at [http://shelx.uni-ac.gwdg.de/SHELX], [http://dx.doi.org/10.1107/S0108767307043930 overview paper])<br />
* moleman, lsqman, ... from [http://xray.bmc.uu.se/usf/ Uppsala Software Factory]<br />
* XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds homepage] and [http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS XDSwiki]<br />
* HKL [http://www.hkl-xray.com homepage]<br />
* [[COOT]]<br />
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki<br />
* [[CCP4mg]]<br />
* [[O]]<br />
* [[ARP/wARP]]<br />
* [[SHARP]] [http://www.globalphasing.com homepage]<br />
* [http://www.solve.lanl.gov/index.html Solve/Resolve]<br />
* [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.<br />
<br />
=== Libraries for crystallography and related areas ===<br />
* [[Clipper]]<br />
* [[cctbx|Crystallographic Toolbox]]<br />
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html]<br />
* [[mmdb]]<br />
<br />
=== Tips and Tricks ===<br />
* [[Finding symmetry elements in P1]]<br />
* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]<br />
<br />
== Teaching crystallography ==<br />
=== [[Crystallography courses on the web]] ===<br />
=== [[Crystallography books]] ===<br />
=== [[Test data sets]] ===<br />
=== The effect of resolution on electron density ===<br />
* James Holton's movie [[https://bl831.als.lbl.gov/~jamesh/movies/resolution.mpeg]]<br />
<br />
== Understanding and extending the properties and limitations of crystallographic computations ==<br />
<br />
=== Ensemble refinement, and molecular dynamics ===<br />
# Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [http://dx.DOI.org/10.1126/science.271.5245.72]<br />
# Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [http://dx.doi.org/10.1016/j.str.2004.02.031]<br />
# Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [http://dx.doi.org/10.1016/j.str.2007.06.019] <br />
# A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [http://dx.doi.org/10.1038/nsb0397-202] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)<br />
<br />
=== Electron microscopy and X-ray ===<br />
# Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [http://dx.doi.org/10.1016/S0969-2126(99)80120-8]<br />
<br />
=== NMR versus X-ray ===<br />
A couple of papers analysing and comparing NMR and X-ray methods/structures:<br />
# Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [http://dx.doi.org/10.1126/science.1502561]<br />
# X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website.<br />
# Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. [http://dx.doi.org/10.1371/journal.pcbi.0020009]</div>ClemensVonrheinhttps://wiki.uni-konstanz.de/ccp4/index.php?title=Scaled_unmerged_data_files&diff=2768Scaled unmerged data files2021-04-23T13:24:20Z<p>ClemensVonrhein: /* autoPROC */</p>
<hr />
<div>== Depositing ==<br />
A deposition to the wwPDB may not only include merged reflection data (i.e. the typical input to the refinement program), but also scaled unmerged data (as part of the<br />
[https://www.wwpdb.org/news/news?year=2021#60638da1931d5660393084c3 Improved support for extended PDBx/mmCIF structure factor files]<br />
announced in 2021).<br />
A PDBx/mmCIF reflection data file with such data can be<br />
<br />
*generated by a MX software suite directly (which is often the preferred way, since it will typically also contain the data quality metrics describing the data) - see e.g. [https://www.globalphasing.com/autoproc/ autoPROC] from [https://www.globalphasnig.com/ Global Phasing],<br />
*generated by [https://project-gemmi.github.io/wasm/mxdepo.html this web app] or the equivalent command-line program, both developed as part of project [https://github.com/project-gemmi/gemmi GEMMI].<br />
<br />
The prerequisite for the latter is a file with scaled unmerged data.<br />
<br />
<br />
Please remember that a full deposition of reflection data will usually contain<br />
* The data that went into the final refinement step (to provide the possibility for validation and re-refinement)<br />
* The output of the refinement program - including map coefficients for the 2mFo-DFc (electron) density map and the mFo-DFc difference density map. This will allow a user to compute the maps exactly as seen by the depositor, i.e. those maps any original model interpretation were based upon.<br />
* (optionally) the scaled and merged data before a final step of data selection, application of a cut-off or re-scaling.<br />
* The scaled and unmerged data discussed on this page.<br />
* (optionally) Additional reflection data that describe for example subsets of the data, different wavelengths or such.<br />
* A set of data quality metrics for each of those separate reflection datablocks (R-values, completeness, redundancy, CC1/2, mean I/sig(I) etc).<br />
<br />
== Where to find scaled unmerged data? ==<br />
<br />
===[http://legacy.ccp4.ac.uk/html/aimless.html Aimless]===<br />
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.<br />
<br />
=== [https://www.globalphasing.com/autoproc/ autoPROC] ===<br />
Individual scaled unmerged data is stored in <code>*unmerged.mtz</code>. However, full deposition-ready PDBx/mmCIF files are already generated (including multiple datablocks with merged and unmerged data) - including the full set of data quality metrics: <code>Data_1_autoPROC_STARANISO_all.cif</code> (for the anisotropic/STARANISO analysed data) and <code>Data_2_autoPROC_TRUNCATE_all.cif</code> (for the traditional/isotropic data). These can be used as-is for deposition and no subsequent format conversion from MTZ is required. Furthermore, no additional extraction of data quality metrics should be necessary. If [https://www.globalphasing.com/buster/ BUSTER] was used for structure refinement, the <code>aB_deposition_combine</code> tool can be used to combine the reflection mmCIF file from refinement with this one from data processing - and transfer the correct set of data quality metrics into the model mmCIF file.<br />
<br />
See also [https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif here] for more details.<br />
<br />
===CCP4i===<br />
i1 has a few tasks that scale data:<br />
<br />
* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).<br />
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.<br />
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.<br />
<br />
===CCP4i2===<br />
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:<br />
<br />
☑ ''output unmerged data as well as merged''<br />
<br />
===CCP4 Cloud===<br />
Saving scaled unmerged data is not supported?<br />
<br />
===dials.scale===<br />
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:<br />
<br />
<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code><br />
<br />
or use dials.export afterwards:<br />
<br />
<code>dials.export scaled.refl scaled.expt</code><br />
<br />
===DUI===<br />
The DIALS User Interface has 8 steps. The last one is ''export'' which writes unmerged MTZ file. The option ''Output Scaled Intensities'' must be checked (default) to write scaled unmerged data.<br />
<br />
===HKL2000===<br />
<br />
The 'no merge original index' macro for SCALEPACK produces a non-standard .sca file. It cannot be used, for example, for structure solution in HKL2000, and therefore gives a warning.<br />
<br />
===iMosflm===<br />
iMosflm can scale data with Aimless. Scaled unmerged MTZ file is written by default since v7.4.0 (soon to be released).<br />
Older versions had option (off by default) to write scaled unmerged data in the SCALEPACK format.<br />
<br />
===SCALA===<br />
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.<br />
<br />
=== [https://staraniso.globalphasing.org STARANISO] ===<br />
See [https://staraniso.globalphasing.org/deposition_about.html here] for up-to-date details regarding deposition and mmCIF files generated already on the [https://staraniso.globalphasing.org STARANISO server].<br />
<br />
===XDS / XSCALE===<br />
Scaled unmerged data from XDS CORRECT and XSCALE is written in the XDS_ASCII.HKL format. The GEMMI converter can use these files directly.<br />
<br />
===xdsme===<br />
<br />
Since xdsme uses XDS/XSCALE, see above.<br />
<br />
===xia2===<br />
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.</div>ClemensVonrheinhttps://wiki.uni-konstanz.de/ccp4/index.php?title=Scaled_unmerged_data_files&diff=2767Scaled unmerged data files2021-04-23T12:33:09Z<p>ClemensVonrhein: /* Depositing */</p>
<hr />
<div>== Depositing ==<br />
A deposition to the wwPDB may not only include merged reflection data (i.e. the typical input to the refinement program), but also scaled unmerged data (as part of the<br />
[https://www.wwpdb.org/news/news?year=2021#60638da1931d5660393084c3 Improved support for extended PDBx/mmCIF structure factor files]<br />
announced in 2021).<br />
A PDBx/mmCIF reflection data file with such data can be<br />
<br />
*generated by a MX software suite directly (which is often the preferred way, since it will typically also contain the data quality metrics describing the data) - see e.g. [https://www.globalphasing.com/autoproc/ autoPROC] from [https://www.globalphasnig.com/ Global Phasing],<br />
*generated by [https://project-gemmi.github.io/wasm/mxdepo.html this web app] or the equivalent command-line program, both developed as part of project [https://github.com/project-gemmi/gemmi GEMMI].<br />
<br />
The prerequisite for the latter is a file with scaled unmerged data.<br />
<br />
<br />
Please remember that a full deposition of reflection data will usually contain<br />
* The data that went into the final refinement step (to provide the possibility for validation and re-refinement)<br />
* The output of the refinement program - including map coefficients for the 2mFo-DFc (electron) density map and the mFo-DFc difference density map. This will allow a user to compute the maps exactly as seen by the depositor, i.e. those maps any original model interpretation were based upon.<br />
* (optionally) the scaled and merged data before a final step of data selection, application of a cut-off or re-scaling.<br />
* The scaled and unmerged data discussed on this page.<br />
* (optionally) Additional reflection data that describe for example subsets of the data, different wavelengths or such.<br />
* A set of data quality metrics for each of those separate reflection datablocks (R-values, completeness, redundancy, CC1/2, mean I/sig(I) etc).<br />
<br />
== Where to find scaled unmerged data? ==<br />
<br />
===[http://legacy.ccp4.ac.uk/html/aimless.html Aimless]===<br />
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.<br />
<br />
=== [https://www.globalphasing.com/autoproc/ autoPROC] ===<br />
Individual scaled unmerged data is stored in <code>*unmerged.mtz</code>. However, full deposition-ready PDBx/mmCIF files are already generated (including multiple datablocks with merged and unmerged data) - including the full set of data quality metrics: <code>Data_1_autoPROC_STARANISO_all.cif</code> (for the anisotropic/STARANISO analysed data) and <code>Data_2_autoPROC_TRUNCATE_all.cif</code> (for the traditional/isotropic data). These can be used as-is for deposition and no subsequent format conversion from MTZ is required. Furthermore, no additional extraction of data quality metrics should be necessary. If [https://www.globalphasing.com/buster/ BUSTER] was used for structure refinement, the <code>aB_deposition_combine</code> tool can be used to combine the reflection mmCIF file from refinement with this one from data processind - and transfer the correct set of data quality metrics into the model mmCIF file.<br />
<br />
See also [https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif here] for more details.<br />
<br />
===CCP4i===<br />
i1 has a few tasks that scale data:<br />
<br />
* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).<br />
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.<br />
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.<br />
<br />
===CCP4i2===<br />
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:<br />
<br />
☑ ''output unmerged data as well as merged''<br />
<br />
===CCP4 Cloud===<br />
Saving scaled unmerged data is not supported?<br />
<br />
===dials.scale===<br />
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:<br />
<br />
<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code><br />
<br />
or use dials.export afterwards:<br />
<br />
<code>dials.export scaled.refl scaled.expt</code><br />
<br />
===DUI===<br />
The DIALS User Interface has 8 steps. The last one is ''export'' which writes unmerged MTZ file. The option ''Output Scaled Intensities'' must be checked (default) to write scaled unmerged data.<br />
<br />
===HKL2000===<br />
<br />
The 'no merge original index' macro for SCALEPACK produces a non-standard .sca file. It cannot be used, for example, for structure solution in HKL2000, and therefore gives a warning.<br />
<br />
===iMosflm===<br />
iMosflm can scale data with Aimless. Scaled unmerged MTZ file is written by default since v7.4.0 (soon to be released).<br />
Older versions had option (off by default) to write scaled unmerged data in the SCALEPACK format.<br />
<br />
===SCALA===<br />
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.<br />
<br />
=== [https://staraniso.globalphasing.org STARANISO] ===<br />
See [https://staraniso.globalphasing.org/deposition_about.html here] for up-to-date details regarding deposition and mmCIF files generated already on the [https://staraniso.globalphasing.org STARANISO server].<br />
<br />
===XDS / XSCALE===<br />
Scaled unmerged data from XDS CORRECT and XSCALE is written in the XDS_ASCII.HKL format. The GEMMI converter can use these files directly.<br />
<br />
===xdsme===<br />
<br />
Since xdsme uses XDS/XSCALE, see above.<br />
<br />
===xia2===<br />
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.</div>ClemensVonrheinhttps://wiki.uni-konstanz.de/ccp4/index.php?title=Scaled_unmerged_data_files&diff=2766Scaled unmerged data files2021-04-23T11:33:26Z<p>ClemensVonrhein: /* Depositing */</p>
<hr />
<div>== Depositing ==<br />
A deposition to the wwPDB may not only include merged reflection data (i.e. the typical input to the refinement program), but also scaled unmerged data (as part of the<br />
[https://www.wwpdb.org/news/news?year=2021#60638da1931d5660393084c3 Improved support for extended PDBx/mmCIF structure factor files]<br />
announced in 2021).<br />
A PDBx/mmCIF reflection data file with such data can be<br />
<br />
*generated by a MX software suite directly (which is often the preferred way, since it will typically also contain the data quality metrics describing the data) - see e.g. [https://www.globalphasing.com/autoproc/ autoPROC] from [https://www.globalphasnig.com/ Global Phasing],<br />
*generated by [https://project-gemmi.github.io/wasm/mxdepo.html this web app] or the equivalent command-line program, both developed as part of project [https://github.com/project-gemmi/gemmi GEMMI].<br />
<br />
The prerequisite for the latter is a file with scaled unmerged data.<br />
<br />
Please remember that a full deposition of reflection data will usually contain<br />
* The data that went into the final refinement step (to provide the possibility for validation and re-refinement)<br />
* The output of the refinement program - including map coefficients for the 2mFo-DFc (electron) density map and the mFo-DFc difference density map. This will allow a user to compute the maps exactly as seen by the depositor, i.e. those maps any original model interpretation were based upon.<br />
* (optionally) the scaled and merged data before a final step of data selection, application of a cut-off or re-scaling.<br />
* The scaled and unmerged data discussed on this page.<br />
* (optionally) Additional reflection data that describe for example subsets of the data, different wavelengths or such.<br />
* A set of data quality metrics for each of those separate reflection datablocks (R-values, completeness, redundancy, CC1/2, mean I/sig(I) etc).<br />
<br />
== Where to find scaled unmerged data? ==<br />
<br />
===Aimless===<br />
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.<br />
<br />
=== autoPROC ===<br />
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file (GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).<br />
<br />
===CCP4i===<br />
i1 has a few tasks that scale data:<br />
<br />
* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).<br />
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.<br />
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.<br />
<br />
===CCP4i2===<br />
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:<br />
<br />
☑ ''output unmerged data as well as merged''<br />
<br />
===CCP4 Cloud===<br />
Saving scaled unmerged data is not supported?<br />
<br />
===dials.scale===<br />
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:<br />
<br />
<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code><br />
<br />
or use dials.export afterwards:<br />
<br />
<code>dials.export scaled.refl scaled.expt</code><br />
<br />
===DUI===<br />
The DIALS User Interface has 8 steps. The last one is ''export'' which writes unmerged MTZ file. The option ''Output Scaled Intensities'' must be checked (default) to write scaled unmerged data.<br />
<br />
===HKL2000===<br />
<br />
The 'no merge original index' macro for SCALEPACK produces a non-standard .sca file. It cannot be used, for example, for structure solution in HKL2000, and therefore gives a warning.<br />
<br />
===iMosflm===<br />
iMosflm can scale data with Aimless. Scaled unmerged MTZ file is written by default since v7.4.0 (soon to be released).<br />
Older versions had option (off by default) to write scaled unmerged data in the SCALEPACK format.<br />
<br />
===SCALA===<br />
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.<br />
<br />
=== StarANISO ===<br />
?<br />
<br />
===XDS / XSCALE===<br />
Scaled unmerged data from XDS CORRECT and XSCALE is written in the XDS_ASCII.HKL format. The GEMMI converter can use these files directly.<br />
<br />
===xdsme===<br />
<br />
Since xdsme uses XDS/XSCALE, see above.<br />
<br />
===xia2===<br />
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.</div>ClemensVonrhein