Publications - Revision history

Randy: /* Primary Citations */ Bringing up to date

2025-11-24T14:54:25Z

‎Primary Citations: Bringing up to date

Randy: Change the rest of the instances of http to https, in preparation for when everything might be https.

2018-12-06T16:27:20Z

Change the rest of the instances of http to https, in preparation for when everything might be https.

Randy: /* Primary Citations */ Add some citations since 2016. Change http to https.

2018-12-06T16:24:40Z

‎Primary Citations: Add some citations since 2016. Change http to https.

Randy: /* Primary Citations */ Add LLGI paper

2016-04-25T13:29:15Z

‎Primary Citations: Add LLGI paper

Airlie at 14:54, 19 January 2015

2015-01-19T14:54:28Z

Randy: /* Primary Citations */ Format LERF citation like the rest (authors after title)

2013-10-21T15:54:17Z

‎Primary Citations: Format LERF citation like the rest (authors after title)

Randy: /* Primary Citations */ Add CCP4 Study Weekend 2013 papers

2013-10-21T15:52:38Z

‎Primary Citations: Add CCP4 Study Weekend 2013 papers

Airlie: /* Reviews */

2013-07-19T13:58:52Z

‎Reviews

Airlie: /* Primary Citations */

2013-07-18T12:20:36Z

‎Primary Citations

Airlie at 10:54, 18 July 2013

2013-07-18T10:54:21Z

← Older revision		Revision as of 14:54, 24 November 2025
Line 26:		Line 26:

	==Primary Citations==		==Primary Citations==
		+
		+	;Likelihood-based interactive local docking into cryo-EM maps in ChimeraX [https://doi.org/10.1107/S2059798324006776 '''Acta Cryst D''']
		+	:Read RJ, Pettersen EF, McCoy AJ, Croll TI, Terwilliger TC, Poon BK, Meng EC, Liebschner D, Adams PD
		+	:Acta Cryst. (2024). D80, 588-598
		+
		+	;Likelihood-based docking of models into cryo-EM maps [https://doi.org/10.1107/S2059798323001602 '''Acta Cryst D''']
		+	:Millán C, McCoy AJ, Terwilliger TC, Read RJ
		+	:Acta Cryst. (2023). D79, 281-289
		+
		+	;Likelihood-based signal and noise analysis for docking of models into cryo-EM maps [https://doi.org/10.1107/S2059798323001596 '''Acta Cryst D''']
		+	:Read RJ, Millán C, McCoy AJ, Terwilliger TC
		+	:Acta Cryst. (2023). D79, 271-280.
		+
		+	;Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE [https://doi.org/10.1107/S2059798322010026 '''Acta Cryst D''']
		+	:Oeffner RD, Croll TI, Millán C, Poon BK, Schlicksup CJ, Read RJ, Terwilliger TC
		+	:Acta Cryst. (2022). D78, 1303-1314
		+
		+	;Implications of AlphaFold2 for crystallographic phasing by molecular replacement [https://doi.org/10.1107/S2059798321012122 '''Acta Cryst D''']
		+	:McCoy AJ, Sammito MD, Read RJ
		+	:Acta Cryst. (2022). D78, 1-13
		+
		+	;Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data [https://doi.org/10.1107/S2059798321004538 '''Acta Cryst D''']
		+	:Hatti KS, McCoy AJ, Read RJ
		+	:Acta Cryst. (2021). D77, 880-893
		+
		+	;Detection of translational noncrystallographic symmetry in Patterson functions [https://doi.org/10.1107/S2059798320016836 '''Acta Cryst D''']
		+	:Caballero I, Sammito MD, Afonine PV, Usón I, Read RJ, McCoy AJ
		+	:Acta Cryst. (2021). D77, 131-141
		+
		+	;Phasertng: directed acyclic graphs for crystallographic phasing [https://doi.org/10.1107/S2059798320014746 '''Acta Cryst D''']
		+	:McCoy AJ, Stockwell DH, Sammito MD, Oeffner RD, Hatti KS, Croll TI, Read RJ
		+	:Acta Cryst. (2021). D77, 1-10
		+
		+	;Measuring and using information gained by observing diffraction data [https://doi.org/10.1107/S2059798320001588 '''Acta Cryst D''']
		+	:Read RJ, Oeffner RD, McCoy AJ
		+	:Acta Cryst. (2020). D76, 238-247
		+
		+	;Factors influencing estimates of coordinate error for molecular replacement [https://doi.org/10.1107/S2059798319015730 '''Acta Cryst D''']
		+	:Hatti KS, McCoy AJ, Oeffner RD, Sammito MD, Read RJ
		+	:Acta Cryst. (2020). D76, 19-27
		+
		+	;Coping with strong translational non-crystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a [https://doi.org/10.1107/S2059798318017825 '''Acta Cryst D''']
		+	:Jamshidiha M, Pérez-Dorado I, Murray JW, Tate EW, Cota E, Read RJ
		+	:Acta Cryst. (2019). D75, 342-353

	;Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement [https://scripts.iucr.org/cgi-bin/paper?cb5100 '''Acta Cryst D''']		;Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement [https://scripts.iucr.org/cgi-bin/paper?cb5100 '''Acta Cryst D''']

@@ Line 1: / Line 1: @@
 ==Citation==
-;Phaser crystallographic software [http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst''']
+;Phaser crystallographic software [https://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst''']
 :McCoy AJ, Grosse-Kunstleve RW,  Adams PD, Winn MD, Storoni LC, Read RJ
 :J. Appl. Cryst. (2007). 40, 658-674
 ==Reviews==
-;Using SAD data in Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']
+;Using SAD data in Phaser [https://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']
 :Read RJ, McCoy AJ
 :Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344
-;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [http://scripts.iucr.org/cgi-bin/paper?ba5142 '''Acta Cryst D''']
+;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [https://scripts.iucr.org/cgi-bin/paper?ba5142 '''Acta Cryst D''']
 :McCoy AJ, Read RJ
 :Acta Cryst. (2010) D66, 458-469.
-;An introduction to molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5108 '''Acta Cryst D''']
+;An introduction to molecular replacement [https://scripts.iucr.org/cgi-bin/paper?ba5108 '''Acta Cryst D''']
 :Evans P, McCoy A
 :Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.
-;Solving structures of protein complexes by molecular replacement with Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5095  '''Acta Cryst D''']
+;Solving structures of protein complexes by molecular replacement with Phaser [https://scripts.iucr.org/cgi-bin/paper?ba5095  '''Acta Cryst D''']
 :McCoy AJ
 :Acta Cryst. (2007). D63, 32-41
-;Liking Likelihood [http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']
+;Liking Likelihood [https://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']
 :McCoy AJ
 :Acta Cryst. (2004). D60, 2169-2183

@@ Line 27: / Line 27: @@
 ==Primary Citations==
-;A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error [http://scripts.iucr.org/cgi-bin/paper?dz5382 '''Acta Cryst D''']
+;Gyre and gimble&#58; a maximum-likelihood replacement for Patterson correlation refinement [https://scripts.iucr.org/cgi-bin/paper?cb5100 '''Acta Cryst D''']
 :Read RJ, McCoy AJ
 :Acta Cryst. (2016). D72, 375-387
-;Phaser.MRage&#58; automated molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5210 '''Acta Cryst D''']
+;Phaser.MRage&#58; automated molecular replacement [https://scripts.iucr.org/cgi-bin/paper?ba5210 '''Acta Cryst D''']
 :Bunkoczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ
 :Acta Cryst. (2013). D69, 2276-2286
-;SCEDS&#58; protein fragments for molecular replacement in Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5209 '''Acta Cryst D''']
+;SCEDS&#58; protein fragments for molecular replacement in Phaser [https://scripts.iucr.org/cgi-bin/paper?ba5209 '''Acta Cryst D''']
 :McCoy AJ, Nicholls RA, Schneider TR
 :Acta Cryst. (2013). D69, 2216-2225
-;Improved estimates of coordinate error for molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5212 '''Acta Cryst D''']
+;Improved estimates of coordinate error for molecular replacement [https://scripts.iucr.org/cgi-bin/paper?ba5212 '''Acta Cryst D''']
 :Oeffner RD, Bunkocz G, McCoy AJ, Read RJ
 :Acta Cryst. (2013). D69, 2209-2215
-;Intensity statistics in the presence of translational non-crystallographic symmetry [http://scripts.iucr.org/cgi-bin/paper?dz5268 '''Acta Cryst D''']
+;Intensity statistics in the presence of translational non-crystallographic symmetry [https://scripts.iucr.org/cgi-bin/paper?dz5268 '''Acta Cryst D''']
 :Read RJ, Adams PD, McCoy AJ
 :Acta Cryst. (2013). D69, 176-183
-;Improvement of molecular replacement models with ''Sculptor'' [http://scripts.iucr.org/cgi-bin/paper?ba5163 '''Acta Cryst D''']
+;Improvement of molecular replacement models with ''Sculptor'' [https://scripts.iucr.org/cgi-bin/paper?ba5163 '''Acta Cryst D''']
 :Bunkoczi G, Read RJ
 :Acta Cryst. (2011). D67, 303-312
-;Likelihood-enhanced fast translation functions [http://scripts.iucr.org/cgi-bin/paper?gx5042 '''Acta Cryst D''']
+;Likelihood-enhanced fast translation functions [https://scripts.iucr.org/cgi-bin/paper?gx5042 '''Acta Cryst D''']
 :McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ
 :Acta Cryst. (2005). D61, 458-464
-;Simple algorithm for a maximum-likelihood SAD function [http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']
+;Simple algorithm for a maximum-likelihood SAD function [https://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']
 :McCoy AJ, Storoni LC,  Read RJ
 :Acta Cryst. (2004). D60, 1220-1228
-;Likelihood-enhanced fast rotation functions [http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D'''] [http://www-structmed.cimr.cam.ac.uk/Personal/randy/pubs/ad5007.pdf '''pdf''']
+;Likelihood-enhanced fast rotation functions [https://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D'''] [http://www-structmed.cimr.cam.ac.uk/Personal/randy/pubs/ad5007.pdf '''pdf''']
 :Storoni LC, McCoy AJ, Read RJ
 :Acta Cryst. (2004). D60, 432-438
-;Pushing the boundaries of molecular replacement with maximum likelihood [http://scripts.iucr.org/cgi-bin/paper?ba5014 '''Acta Cryst D''']
+;Pushing the boundaries of molecular replacement with maximum likelihood [https://scripts.iucr.org/cgi-bin/paper?ba5014 '''Acta Cryst D''']
 :Read RJ
 :Acta Cryst. (2001). D57, 1373-1382

← Older revision		Revision as of 13:29, 25 April 2016
Line 26:		Line 26:

	==Primary Citations==		==Primary Citations==
		+
		+	;A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error [http://scripts.iucr.org/cgi-bin/paper?dz5382 '''Acta Cryst D''']
		+	:Read RJ, McCoy AJ
		+	:Acta Cryst. (2016). D72, 375-387

	;Phaser.MRage: automated molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5210 '''Acta Cryst D''']		;Phaser.MRage: automated molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5210 '''Acta Cryst D''']

@@ Line 1: / Line 1: @@
 ==Citation==
 ;Phaser crystallographic software [http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst''']
@@ Line 6: / Line 5: @@
 ==Reviews==
 ;Using SAD data in Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']
 :Read RJ, McCoy AJ

← Older revision		Revision as of 15:52, 21 October 2013
Line 31:		Line 31:

	==Primary Citations==		==Primary Citations==
		+
		+	;Phaser.MRage: automated molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5210 '''Acta Cryst D''']
		+	:Bunkoczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ
		+	:Acta Cryst. (2013). D69, 2276-2286
		+
		+	;SCEDS: protein fragments for molecular replacement in Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5209 '''Acta Cryst D''']
		+	:McCoy AJ, Nicholls RA, Schneider TR
		+	:Acta Cryst. (2013). D69, 2216-2225
		+
		+	;Improved estimates of coordinate error for molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5212 '''Acta Cryst D''']
		+	:Oeffner RD, Bunkocz G, McCoy AJ, Read RJ
		+	:Acta Cryst. (2013). D69, 2209-2215

	;Intensity statistics in the presence of translational non-crystallographic symmetry [http://scripts.iucr.org/cgi-bin/paper?dz5268 '''Acta Cryst D''']		;Intensity statistics in the presence of translational non-crystallographic symmetry [http://scripts.iucr.org/cgi-bin/paper?dz5268 '''Acta Cryst D''']