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NCMI Workshop on Single Particle Reconstruction, Validation and Analysis

March 14 - 17, 2011

This page contains the workshop schedule, and will contain the PDFs of each of the presentations at the workshop. Speakers are asked to upload their presentations sometime before the beginning of their talk (preferably as far in advance as possible).

The data and software required for participation in the tutorial sessions can be found at: Workshop2011.

Information on the location of the workshop and where to park is here: Ws2011/Location

The main workshop page is here: http://ncmi.bcm.edu/ncmi/events/workshops/workshops_114

Note that PGH216 is an overflow room for the lectures in case the lecture hall becomes full for the talks. During the tutorial sessions, there will be plenty of seats in PGH232.

Mon Mar 14, 2011

Theme - Single particle reconstruction

8:00 - 8:50	Registration	Outside PGH 232
8:50 - 9:10	Opening remarks/Introduction to Workshop	PGH232	Dr. Steve Ludtke
9:10 - 10:00	Cryo-EM Essentials	PGH232	Dr. Wah Chiu
10:00 - 10:50	Image processing theory	PGH232	Dr. Richard Henderson
11:00 - 11:20	Coffee Break
11:20 - 12:30	Tutorial 1 - Getting started with EMAN2, CTF & class-averages	PGH232&200	Dr. Steve Ludtke
	Tutorial 1 - Slides from presentation
12:30 - 1:30	Lunch
1:30 - 3:00	Tutorial 1, contd - Initial models	PGH232&200	Dr. Steve Ludtke
3:00 - 3:20	Coffee Break
3:20 - 5:00	Tutorial 1, contd - First refinement & other issues	PGH232&200	Dr. Steve Ludtke
5:00 - 6:00	Research Lecture: Structural studies of TriC/CCT	PGH232	Dr. Yao Cong
6:00 - 9:00	Dinner onsite - with participant short talks	PGH232

Tue Mar 15, 2011

Theme - Helices & Heterogeneity

9:00 - 10:00	Helical filaments, heterogeneity and polymorphisms	PGH232	Dr. Edward Egelman
10:00 - 10:20	Coffee Break
10:20 - 11:20	Identification of conformational states using resampling	PGH232	Dr. Pawel Penczek
11:30 - 12:30	Tutorial 2 - Chimera	PGH232&200	Tom Goddard
12:30 - 1:30	Lunch
1:30 - 3:00	Tutorial 3 - Evaluating refinements, heterogeneity, etc.	PGH232&200	Dr. Steve Ludtke
	Tutorial 3 - Presentation slides for tutorial session
3:00 - 3:15	Coffee Break
3:15 - 5:00	Tutorial 4 - Introduction to identification of conformational states in SPARX	PGH232&200	Dr. Pawel Penczek
5:15 - 6:15	Research Talk - Multiple states of a chaperonin and a method for analyzing heterogeneous conformations in cryo-EM	PGH232	Dr. Junjie (George) Zhang
6:30 - 9:00	Dinner	UH Library

Wed, Mar 16, 2011

Theme - Related methods

8:50 - 9:15	Tutorial 5 - Quick morning tutorial session	PGH232&200	Stephen Murray
9:15 - 10:00	Single particle tomography	PGH232	Dr. Mike Schmid
10:10 - 10:30	Coffee Break
10:30 - 11:00	EMDatabank.org & Data Archival Tutorial/Guide	PGH232	Dr. Cathy Lawson
11:00 - 11:45	Tutorial 6 - Segmentation with Segger	PGH200&232	Dr. Greg Pintilie
11:45 - 12:45	Lunch
12:45 - 3:00	Tutorial 5 cont'd - Frealign, multirefine, etc.	PGH200&232	Stephen Murray & Dr. Steve Ludtke
3:00 - 3:30	Coffee Break
3:30 - 5:00	Tutorial 7 - Single Particle Tomography in EMAN2 Short PPT intro	PGH200&232	Jesus Galaz & Dr. John Flanagan
5:10 - 6:10	Research Talk - Structural studies of Calcium release channels	PGH232	Dr. Irina Serysheva
7:00 - 9:00	Workshop Banquet Bus leaves U of H at 6:30 !	Fung’s Kitchen

Thu, Mar 17, 2011

Theme: Validation & Modeling

9:00 - 10:00	Methods for Validation of Cryo-EM Maps	PGH232	Dr. Richard Henderson
10:00 - 10:30	Coffee Break
10:30 - 11:30	Tutorial 8: Real-space Refinement of Atomic Models in DireX	PGH200/232	Dr. Gunnar Schroeder
11:30 - 12:15	Tutorial 9: The EMEN2 Electronic Notebook and OODB	PGH200/232	Ian Rees
12:15 - 1:00	Lunch
1:00 - 2:30	Tutorial 10: Introduction to Rosetta	PGH200/232	Dr. Yao Cong
2:30 - 3:00	Coffee Break
3:00 - 4:30	Tutorial 11: Model Building and Analysis with Gorgon	PGH200/232	Dr. Matt Baker
4:30 - 5:30	Workshop wrap-up, final discussion

Workshop Ends

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-Mon Mar 14, 2011
+== NCMI Workshop on Single Particle Reconstruction, Validation and Analysis ==
=== March 14 - 17, 2011 ===
This page contains the workshop schedule, and will contain the PDFs of each of the presentations at the workshop. Speakers are asked to upload their presentations sometime before the beginning of their talk (preferably as far in advance as possible).
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-Theme - Single particle reconstruction
||8:00 - 8:50 ||Registration ||Outside PGH 200 ||
||8:50 - 9:10 ||Opening remarks/Introduction to Workshop ||PGH200 ||Dr. Steve Ludtke ||
||9:10 - 10:00 ||[[attachment:1_1_chiu_microscopy.pdf|Introduction to transmission electron microscopy]] ||PGH200 ||Dr. Wah Chiu ||
||10:00 - 10:50 ||[[attachment:1_2_henderson_image_processing.pdf|Image processing theory]] ||PGH200 ||Dr. Richard Henderson ||
||11:00 - 11:20 ||Coffee Break ||
||11:20 - 12:30 ||[[attachment:1_3_ludtke_EMAN2.pdf|Tutorial 1 - Getting started with EMAN2, CTF & class-averages]] ||PGH232&200 ||Dr. Steve Ludtke ||
||12:30 - 1:30 ||Lunch ||
+The data and software required for participation in the tutorial sessions can be found at: [[Workshop2011]].

Information on the location of the workshop and where to park is here: [[Ws2011/Location]]

The main workshop page is here: http://ncmi.bcm.edu/ncmi/events/workshops/workshops_114

Note that PGH216 is an overflow room for the lectures in case the lecture hall becomes full for the talks. During the tutorial sessions, there will be plenty of seats in PGH232.

'''Mon Mar 14, 2011'''

''Theme - Single particle reconstruction''
||8:00 - 8:50 ||Registration ||Outside PGH 232 || ||
||8:50 - 9:10 ||Opening remarks/Introduction to Workshop ||PGH232 ||Dr. Steve Ludtke ||
||9:10 - 10:00 ||[[attachment:1_1-Chiu_CryoEM.pdf|Cryo-EM Essentials]] ||PGH232 ||Dr. Wah Chiu ||
||10:00 - 10:50 ||[[attachment:1_2_henderson_image_processing.pdf|Image processing theory|&do=get]] ||PGH232 ||Dr. Richard Henderson ||
||11:00 - 11:20 ||Coffee Break || || ||
||11:20 - 12:30 ||[[attachment:1_3_ludtke_EMAN2.pdf|Tutorial 1 - Getting started with EMAN2, CTF & class-averages|&do=get]] ||PGH232&200 ||Dr. Steve Ludtke ||
|| ||[[attachment:1_3_ludtke_EMAN2_slides.pdf|Tutorial 1 - Slides from presentation|&do=get]] || || ||
||12:30 - 1:30 ||Lunch || || ||
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+Line 25:
-||3:00 - 3:20 ||Coffee Break ||
+||3:00 - 3:20 ||Coffee Break || || ||
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+Line 27:
-||5:00 - 6:00 ||[[attachment:1_4_cong_TriC-CCT.pdf|Research Lecture: Structural studies of TriC/CCT]] ||PGH200 ||Dr. Yao Cong ||
||6:00 - 9:00 ||Dinner onsite - with participant short talks ||PGH200 ||
+||5:00 - 6:00 ||[[attachment:1_4_cong_TriC-CCT.pdf|Research Lecture: Structural studies of TriC/CCT]] ||PGH232 ||Dr. Yao Cong ||
||6:00 - 9:00 ||Dinner onsite - with participant short talks ||PGH232 || ||
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-Tue Mar 15, 2011
+'''Tue Mar 15, 2011'''
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-Theme - Helices & Heterogeneity
||9:00 - 10:00 ||[[attachment:2_1_egelman_IHRSR.pdf|Helical filaments, heterogeneity and polymorphisms]] ||PGH200 ||Dr. Edward Egelman ||
||10:00 - 10:20 ||Coffee Break ||
||10:20 - 11:20 ||[[attachment:2_2_penczek_conformation.pdf|Identification of conformational states using resampling]] ||PGH200 ||Dr. Pawel Penczek ||
+''Theme - Helices & Heterogeneity''
||9:00 - 10:00 ||[[attachment:2_1_egelman_IHRSR.pdf|Helical filaments, heterogeneity and polymorphisms]] ||PGH232 ||Dr. Edward Egelman ||
||10:00 - 10:20 ||Coffee Break || || ||
||10:20 - 11:20 ||[[attachment:2_2_penczek_conformation.pdf|Identification of conformational states using resampling]] ||PGH232 ||Dr. Pawel Penczek ||
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-||12:30 - 1:30 ||Lunch ||
||1:30 - 3:00 ||[[attachment:2_4_ludtke_EMAN2.pdf|Tutorial 3 - Evaluating refinements, heterogeneity, etc.]] ||PGH232&200 ||Dr. Steve Ludtke ||
||3:00 - 3:15 ||Coffee Break ||
+||12:30 - 1:30 ||Lunch || || ||
||1:30 - 3:00 ||[[attachment:2_4_ludtke_EMAN2.pdf|Tutorial 3 - Evaluating refinements, heterogeneity, etc.|&do=get]] ||PGH232&200 ||Dr. Steve Ludtke ||
|| ||[[attachment:2_4a_ludtke_EMAN2.pdf|Tutorial 3 - Presentation slides for tutorial session|&do=get]] || || ||
||3:00 - 3:15 ||Coffee Break || || ||
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-||5:15 - 6:15 ||[[attachment:2_6_zhang_mmcpn.pdf|Research Talk - Multiple states of a chaperonin and a method for analyzing heterogeneous conformations in cryo-EM]] ||PGH200 ||Dr. Junjie (George) Zhang ||
||6:30 - 9:00 ||Dinner ||UH Library ||
+||5:15 - 6:15 ||[[attachment:2_6_zhang_mmcpn.pdf|Research Talk - Multiple states of a chaperonin and a method for analyzing heterogeneous conformations in cryo-EM]] ||PGH232 ||Dr. Junjie (George) Zhang ||
||6:30 - 9:00 ||Dinner ||UH Library || ||
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-Wed, Mar 16, 2011
+'''Wed, Mar 16, 2011'''
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+Line 53:
-Theme - Related methods
+''Theme - Related methods''
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+Line 55:
-||9:15 - 10:00 ||[[attachment:3_2_schmid_spt.pdf|Single particle tomography]] ||PGH200 ||Dr. Mike Schmid ||
||10:10 - 10:30 ||Coffee Break ||
||10:30 - 11:00 ||[[attachment:3_3_lawson_PDB.pdf|EMDatabank.org & Data Archival]] ||PGH200 ||Dr. Cathy Lawson ||
+||9:15 - 10:00 ||[[attachment:3_2_schmid_spt.pdf|Single particle tomography]] ||PGH232 ||Dr. Mike Schmid ||
||10:10 - 10:30 ||Coffee Break || || ||
||10:30 - 11:00 ||[[attachment:3_3_lawson_PDB.pdf|EMDatabank.org & Data Archival]]  [[attachment:3_3_lawson_EMdepGuide.pdf|Tutorial/Guide]] ||PGH232 ||Dr. Cathy Lawson ||
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+Line 59:
-||11:45 - 12:45 ||Lunch ||
||12:45 - 3:00 ||Tutorial 5 cont'd - Frealign, multirefine, etc. ||PGH200&232 ||Dr. Steve Ludtke & Stephen Murray ||
||3:00 - 3:30 ||Coffee Break ||
||3:30 - 5:00 ||[[attachment:3_5_montoya_spt.pdf|Tutorial 7 - Single Particle Tomography in EMAN2]] ||PGH200&232 ||Jesus Montoya & Dr. John Flanagan ||
||5:10 - 6:10 ||[[attachment:3_6_serysheva_cachannels.pdf|Research Talk - Structural studies of Calcium release channels]] ||PGH200&232 ||Dr. Irina Serysheva ||
||7:00 - 9:00 ||Workshop Banquet '''Bus leaves U of H at 6:30 !''' ||Fung’s Kitchen||
+||11:45 - 12:45 ||Lunch || || ||
||12:45 - 3:00 ||Tutorial 5 cont'd - Frealign, multirefine, etc. ||PGH200&232 ||Stephen Murray & Dr. Steve Ludtke ||
||3:00 - 3:30 ||Coffee Break || || ||
||3:30 - 5:00 ||[[attachment:3_5_galaz_spt.pdf|Tutorial 7 - Single Particle Tomography in EMAN2]]  [[attachment:3_5_galaz_spt_ppt.pdf|Short PPT intro]]||PGH200&232 ||Jesus Galaz & Dr. John Flanagan ||
||5:10 - 6:10 ||Research Talk - Structural studies of Calcium release channels ||PGH232 ||Dr. Irina Serysheva ||
||7:00 - 9:00 ||Workshop Banquet '''Bus leaves U of H at 6:30 !''' ||[[http://www.fungskitchen.com|Fung’s Kitchen]] || ||
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-Thu, Mar 17, 2011
+'''Thu, Mar 17, 2011'''
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-Theme: Validation & Modeling
||9:00 - 10:00 ||[[attachment:4_1_henderson_validation.pdf|Methods for Validation of Cryo-EM Maps]] ||PGH200 ||Dr. Richard Henderson ||
||10:00 - 10:30 ||Coffee Break ||
||10:30 - 11:30 ||[[attachment:4_2_schroeder_direx.pdf|Real-space Refinement of Atomic Models in DireX]] ||PGH200/232 ||Dr. Gunnar Schroeder ||
||11:30 - 12:15 ||[[attachment:4_3_rees_emen2.pdf|The EMEN2 Electronic Notebook and OODB]] ||PGH200/232 ||Ian Rees ||
||12:15 - 1:00 ||Lunch ||
||1:00 - 2:30 ||[[attachment:4_4_cong_rosetta.pdf|Introduction to Rosetta]] ||PGH200/232 ||Dr. Yao Cong ||
||2:30 - 3:00 ||Coffee Break ||
||3:00 - 4:30 ||[[attachment:4_5_baker_gorgon.pdf|Model Building and Analysis with Gorgon]] ||PGH200/232 ||Dr. Matt Baker ||
||4:30 - 5:30 ||Workshop wrap-up, final discussion ||
+''Theme: Validation & Modeling''
||9:00 - 10:00 ||[[attachment:4_1_henderson_validation.pdf|Methods for Validation of Cryo-EM Maps]] ||PGH232 ||Dr. Richard Henderson ||
||10:00 - 10:30 ||Coffee Break || || ||
||10:30 - 11:30 ||Tutorial 8: [[attachment:4_2_schroeder_direx.pdf|Real-space Refinement of Atomic Models in DireX]] ||PGH200/232 ||Dr. Gunnar Schroeder ||
||11:30 - 12:15 ||Tutorial 9: [[attachment:4_3_rees_emen2.pdf|The EMEN2 Electronic Notebook and OODB]] ||PGH200/232 ||Ian Rees ||
||12:15 - 1:00 ||Lunch || || ||
||1:00 - 2:30 ||Tutorial 10: [[attachment:4_4_cong_rosetta.pdf|Introduction to Rosetta]] ||PGH200/232 ||Dr. Yao Cong ||
||2:30 - 3:00 ||Coffee Break || || ||
||3:00 - 4:30 ||Tutorial 11: [[attachment:4_5_baker_gorgon.pdf|Model Building and Analysis with Gorgon]] ||PGH200/232 ||Dr. Matt Baker ||
||4:30 - 5:30 ||Workshop wrap-up, final discussion || ||
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-''Note: Wah will host a dinner for any speakers who will be around Thurs evening''