User contributions
From Phaserwiki
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- 10:53, 20 June 2018 (diff | hist) . . (+141) . . Keywords (→link=OUTLIER: Document INFO subkey of OUTLIER command)
- 20:23, 12 June 2018 (diff | hist) . . (+26) . . Keywords (→link=TRANSLATION: Add setTRAN_PACK_NUMB command to Python section)
- 14:10, 30 April 2018 (diff | hist) . . (+258) . . Keywords (Add FIND defaults.)
- 19:55, 26 April 2018 (diff | hist) . . (+106) . . Keywords (→link=TRANSLATION: Clarify that full search should probably not be used.)
- 19:53, 26 April 2018 (diff | hist) . . (+84) . . Keywords (→link=TARGET: Clarify regions searched for brute rotation and translation searches, and how those are specified.)
- 19:50, 26 April 2018 (diff | hist) . . (+511) . . Keywords (→link=ROTATE: Clarify when (and mostly when not) the brute-force rotation function is relevant.)
- 10:20, 26 April 2018 (diff | hist) . . (+699) . . Molecular Replacement (→How to Define Composition: Clarify numbers of copies, mixing different composition specifications, importance of specifying everything.)
- 10:05, 26 April 2018 (diff | hist) . . (+1,290) . . Molecular Replacement (Add section on How to Define Solutions, to emphasise the difference between composition and search.)
- 09:50, 26 April 2018 (diff | hist) . . (0) . . Molecular Replacement (→How to Define Composition: Move composition by sequence (preferred option) higher in list)
- 21:06, 22 March 2018 (diff | hist) . . (+143) . . Keywords (→Expert Keywords: Add INFO keyword)
- 13:10, 19 February 2018 (diff | hist) . . (+583) . . Keyword Example Scripts (Clarify how to run keyword scripts from Windows.) (current)
- 20:45, 16 February 2018 (diff | hist) . . (+281) . . Keyword Example Scripts (Add instructions about sourcing scripts.)
- 18:21, 14 December 2017 (diff | hist) . . (0) . . Keywords (→link=TRANSLATION: fix spelling)
- 12:15, 13 December 2017 (diff | hist) . . (+78) . . Keywords (→link=PACK: Discourage use of PACK SELECT ALL)
- 11:14, 12 December 2017 (diff | hist) . . (+12) . . Python Example Scripts (→Anisotropy Correction: Change example script to include the new resharpen Boolean, set by default to True) (current)
- 16:54, 2 October 2017 (diff | hist) . . (0) . . m Keywords (→link=SOLUTION: Correct spelling)
- 14:36, 2 September 2017 (diff | hist) . . (+329) . . Top Ten Tips (Add links and citations for sequence alignment tools) (current)
- 12:36, 17 February 2017 (diff | hist) . . (+1) . . Keywords (→link=PACK: Update packing cutoff default)
- 12:20, 11 November 2016 (diff | hist) . . (0) . . Keywords (→link=ELLG: Update eLLG target default)
- 12:43, 31 October 2016 (diff | hist) . . (-1) . . m Keywords (→link=SEARCH: Remove superfluous close square brace)
- 12:41, 31 October 2016 (diff | hist) . . (-256) . . Keywords (→link=SEARCH: Bring up to date with current syntax, match orders of descriptions)
- 10:23, 25 August 2016 (diff | hist) . . (+205) . . Keyword Example Scripts (→Building an Ensemble from Coordinates: Remove reference to non-existent table, and mention using Ensembler to trim NMR ensembles.)
- 09:35, 3 June 2016 (diff | hist) . . (+94) . . Keywords (→link=TARGET: Point out that extra LABIN command is needed for PHASED translation target.)
- 12:22, 3 May 2016 (diff | hist) . . (-10) . . m Keywords (→link=LABIN: Minor wording changes)
- 14:29, 25 April 2016 (diff | hist) . . (+226) . . Publications (→Primary Citations: Add LLGI paper)
- 09:46, 22 April 2016 (diff | hist) . . (+1,029) . . MR using CCP4i:TOXD (Describe the use of alternative models (instead of ensembles) more clearly.)
- 16:44, 9 April 2016 (diff | hist) . . (+51) . . SAD using CCP4i (Suggest using Rfree flag in ARP/wARP, simplify how to specify HLA/B/C/D)
- 12:16, 6 April 2016 (diff | hist) . . (-505) . . Tutorials (Delete reference to Phubuntu, which is no longer relevant.) (current)
- 12:15, 6 April 2016 (diff | hist) . . (-505) . . Downloads (Delete reference to Phubuntu, which is no longer relevant.)
- 10:56, 6 April 2016 (diff | hist) . . (+29) . . Combined MR-SAD using CCP4i (Suggest using Rfree flags in ARP/wARP.)
- 19:40, 5 April 2016 (diff | hist) . . (+267) . . Combined MR-SAD using CCP4i (Suggest using sculptor on the goat model.)
- 17:24, 5 April 2016 (diff | hist) . . (+1,082) . . MR using CCP4i:TOXD (Update to use Sculptor and Ensembler)
- 15:03, 5 April 2016 (diff | hist) . . (+114) . . MR using keyword input (→Searching for more than one molecule: Correct old idea that SEARCH order in script matters.)
- 14:56, 5 April 2016 (diff | hist) . . (-15) . . MR using keyword input (→Adding to the Script: Update script to continue to work, now that multiple PDB files can't be added to ensemble on a single line.)
- 14:43, 5 April 2016 (diff | hist) . . (+272) . . MR using keyword input (→Sample Script: Mention preference for intensities.)
- 16:22, 15 February 2016 (diff | hist) . . (-2) . . Molecular Replacement (→Annotation: Clarify RF++)
- 02:15, 16 January 2016 (diff | hist) . . (+914) . . FAQ (Add warning about the common mistake of using Phaser to "verify" a refined model.) (current)
- 17:19, 27 November 2015 (diff | hist) . . (+1) . . m Keywords (→link=PURGE: Fix spelling)
- 15:56, 25 November 2015 (diff | hist) . . (+97) . . Keywords (→link=MODE: Add mode MR_ELLG)
- 15:51, 25 November 2015 (diff | hist) . . (+44) . . Modes (→Modes: Add sample Python call to mode MR_ELLG)
- 15:48, 25 November 2015 (diff | hist) . . (+240) . . Modes (→Modes: Add mode MR_ELLG)
- 14:05, 25 November 2015 (diff | hist) . . (+424) . . Keywords (→link=TNCS: Update TNCS commands)
- 21:38, 4 November 2015 (diff | hist) . . (+6) . . Python Example Scripts (→Normal Mode Analysis: Fix syntax for NMA, but this still crashes because the modes and the pdb files are not in one-to-one correspondence.)
- 22:33, 3 November 2015 (diff | hist) . . (+4) . . Python Example Scripts (→Anisotropy Correction: Change setREFL_ID to setLABI_F_SIGF)
- 22:09, 3 November 2015 (diff | hist) . . (+7) . . Python Example Scripts (→Translational NCS Analysis: Change setREFL to setREFL_F_SIGF)
- 22:02, 3 November 2015 (diff | hist) . . (+7) . . Python Example Scripts (→Anisotropy Correction: Change setREFL to setREFL_F_SIGF)
- 22:01, 3 November 2015 (diff | hist) . . (+2) . . m Python Example Scripts (→Reading MTZ Files for Experimental Phasing: Comment out name of script in script)
- 21:59, 3 November 2015 (diff | hist) . . (+1) . . Python Example Scripts (→Automated Molecular Replacement: Comment out name of beta_blip_auto.py script in script)
- 21:59, 3 November 2015 (diff | hist) . . (+7) . . Python Example Scripts (→Automated Molecular Replacement: Change setREFL to setREFL_F_SIGF)
- 13:54, 30 October 2015 (diff | hist) . . (0) . . Keywords (→link=HAND: Description of "ON" and "OFF" was reversed)
- 11:33, 8 October 2015 (diff | hist) . . (+11) . . Keywords (→link=TARGET: Minor correction to available rot and tra targets)
- 16:04, 29 June 2015 (diff | hist) . . (+1) . . m Keywords (→link=TNCS: RMS has to be RMSD in TNCS parser)
- 09:57, 10 June 2015 (diff | hist) . . (+38) . . Keywords (→link=OCCUPANCY: Update defaults to agree with current code)
- 09:49, 10 June 2015 (diff | hist) . . (0) . . m Keywords (→link=PACK: typo)
- 09:43, 10 June 2015 (diff | hist) . . (+94) . . Keywords (→link=SEARCH: Clarify pruning algorithm.)
- 08:38, 19 May 2015 (diff | hist) . . (+359) . . Molecular Replacement (→Has Phaser Solved It?: Clarify interpretation of RFZ.)
- 14:58, 14 May 2015 (diff | hist) . . (+174) . . Keywords (→link=PARTIAL: Clarify necessity to carry out MR before MR-SAD.)
- 16:23, 3 February 2015 (diff | hist) . . (+13) . . Keywords (→link=SOLPARAMETERS: Show MINSIGA in equation.)
- 16:18, 3 February 2015 (diff | hist) . . (-47) . . Keywords (→link=SOLPARAMETERS: Replace "s" by "1/d")
- 16:15, 3 February 2015 (diff | hist) . . (+131) . . Keywords (→link=SOLPARAMETERS: Add equation for solvent term for Sigma(A) curve)
- 20:44, 11 November 2014 (diff | hist) . . (+310) . . Molecular Replacement (→Translational Non-crystallographic Symmetry: Some modifications and clarifications)
- 10:48, 11 August 2014 (diff | hist) . . (+321) . . Keywords (→link=PURGE: Clarify interaction with PEAKS command.)
- 10:44, 11 August 2014 (diff | hist) . . (+258) . . Keywords (→link=PEAKS: Clarify that PURGE is usually the command to use.)
- 14:56, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Logfile Handling: Replace setLABI with setLABI_F_SIGF)
- 14:55, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Translational NCS Analysis: Replace setLABI with setLABI_F_SIGF)
- 14:55, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Cell Content Analysis: Replace setLABI with setLABI_F_SIGF)
- 14:54, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Anisotropy Correction: Replace setLABI with setLABI_F_SIGF)
- 14:53, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Automated Molecular Replacement: Replace setLABI with setLABI_F_SIGF)
- 14:53, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Reading MTZ Files for Molecular Replacement: Replace setLABI with setLABI_F_SIGF)
- 15:06, 29 May 2014 (diff | hist) . . (+53) . . Keywords (→link=BFACTOR: Correct definition of BFACTOR REFINE SIGMA, update default for SIGMA)
- 10:02, 28 May 2014 (diff | hist) . . (+1) . . Keywords (→link=MACTNCS: Correct syntax, with VRMS instead of VAR)
- 13:25, 23 April 2014 (diff | hist) . . (+158) . . Keywords (→link=ENSEMBLE: Provide guess for RMS for EM maps.)
- 19:14, 10 April 2014 (diff | hist) . . (+772) . . SAD using CCP4i (Add step to carry on building from very incomplete initial model)
- 13:18, 9 December 2013 (diff | hist) . . (-214) . . Molecular Replacement (→"rlist" Files: Remove discussion of degenerate translation search, which is no longer supported.)
- 13:17, 9 December 2013 (diff | hist) . . (-447) . . Molecular Replacement (→"sol" Files: Remove discussion of degenerate 3DIM and 5DIM cases, no longer supported.)
- 13:14, 9 December 2013 (diff | hist) . . (-133) . . Molecular Replacement (→How to Define Solutions: Remove mention of degenerate translation functions, which are no longer supported.)
- 13:12, 9 December 2013 (diff | hist) . . (-542) . . Keyword Example Scripts (→Brute Translation Function: Remove script for degenerate translation function, which is no longer supported.)
- 13:11, 9 December 2013 (diff | hist) . . (-309) . . Keyword Example Scripts (→"rlist" Files: Remove discussion of degenerate translation search, which is no longer supported.)
- 13:09, 9 December 2013 (diff | hist) . . (-365) . . Keyword Example Scripts (→"sol" Files: Remove discussion of degenerate 3DIM and 5DIM cases, no longer supported.)
- 11:54, 4 December 2013 (diff | hist) . . (+26) . . FAQ (Mention st9bad_alloc so that people with out of memory problems will find this web page.)
- 12:26, 2 December 2013 (diff | hist) . . (+194) . . FAQ (Add suggestion to cut final refinement resolution to reduce memory usage if necessary.)
- 16:54, 21 October 2013 (diff | hist) . . (-2) . . m Publications (→Primary Citations: Format LERF citation like the rest (authors after title))
- 16:52, 21 October 2013 (diff | hist) . . (+634) . . Publications (→Primary Citations: Add CCP4 Study Weekend 2013 papers)
- 08:40, 8 October 2013 (diff | hist) . . (+170) . . Molecular Replacement (→What to do in Difficult Cases: Note that brute rotation function can now be used within automated pipeline)
- 08:36, 8 October 2013 (diff | hist) . . (+443) . . FAQ (Update discussion of negative LLG to mention VRMS refinement.)
- 09:11, 22 August 2013 (diff | hist) . . (+4) . . Keywords (→link=SOLPARAMETERS: Add "USE" subkey to default definition for BULK)
- 11:40, 5 August 2013 (diff | hist) . . (+126) . . Keywords (→link=RFACTOR: Note that this test also applies to judging success in MR_ATOM)
- 11:38, 5 August 2013 (diff | hist) . . (+19) . . Keywords (→link=SOLUTION: Mention Euler angle convention here.)
- 11:37, 5 August 2013 (diff | hist) . . (+218) . . Molecular Replacement (→Annotation: Add explanation of Euler angle convention.)
- 10:21, 4 August 2013 (diff | hist) . . (-2) . . Keywords (→link=RFACTOR: Change RESHARP to RFACTOR to RFACTOR description)
- 13:59, 28 June 2013 (diff | hist) . . (0) . . Keywords (→link=TRANSLATE: Footnotes didn't correspond to superscripts)
- 13:55, 28 June 2013 (diff | hist) . . (+2) . . m Keywords (→link=TRANSLATE: add spaces)
- 13:54, 28 June 2013 (diff | hist) . . (+7) . . Keywords (→link=ROTATE: Need VOLUME subkey in ROTATE AROUND option)
- 14:36, 25 June 2013 (diff | hist) . . (-135) . . FAQ (Update advice on memory consumption)
- 22:51, 11 April 2013 (diff | hist) . . (+7) . . m SAD using CCP4i (formatting)
- 22:25, 11 April 2013 (diff | hist) . . (+84) . . SAD using CCP4i (A few more changes to match the current SAD pipeline.)
- 17:03, 10 April 2013 (diff | hist) . . (+726) . . SAD using CCP4i (Update to describe Phaser pipeline instead of old standalone Phaser-EP GUI)
- 17:58, 19 January 2013 (diff | hist) . . (+62) . . Publications (→Primary Citations: Add link to tNCS statistics PDF)
- 17:57, 19 January 2013 (diff | hist) . . (+149) . . Publications (→Primary Citations: Add tNCS statistics paper (add link once file is uploaded))
- 20:15, 23 November 2012 (diff | hist) . . (-2) . . MR using CCP4i:BETA/BLIP (Update for current version of Phaser) (current)
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