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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	[[attachment:1_3_ludtke_EMAN2.pdf\|Tutorial 1 - Getting started with EMAN2, CTF & class-averages	&do=get]]	PGH232&200	Dr. Steve Ludtke
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	[[attachment:2_2_penczek_conformation.pdf\|Identification of conformational states using resampling	&do=get]]	PGH232	Dr. Pawel Penczek
11:30 - 12:30	[[attachment:2_3_goddard_chimera.pdf\|Tutorial 2 - Chimera	&do=get]]	PGH232&200	Tom Goddard
12:30 - 1:30	Lunch
1:30 - 3:00	Tutorial 3 - Evaluating refinements, heterogeneity, etc.	PGH232&200	Dr. Steve Ludtke
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	[[attachment:3_3_lawson_PDB.pdf\|EMDatabank.org & Data Archival	&do=get]] Tutorial/Guide	PGH232	Dr. Cathy Lawson
11:00 - 11:45	[[attachment:3_4_pintilie_segger.pdf\|Tutorial 6 - Segmentation with Segger	&do=get]]	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	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	Real-space Refinement of Atomic Models in DireX	PGH200/232	Dr. Gunnar Schroeder
11:30 - 12:15	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	&do=get]]	PGH200/232	Dr. Yao Cong
2:30 - 3:00	Coffee Break
3:00 - 4:30	Model Building and Analysis with Gorgon	PGH200/232	Dr. Matt Baker
4:30 - 5:30	Workshop wrap-up, final discussion

Workshop Ends

Note: Wah will host a dinner for any speakers who will be around Thurs evening

-  ⇤ ← Revision 2 as of 2011-03-08 20:41:12 → 
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-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-Mon Mar 14, 2011
+== NCMI Workshop on Single Particle Reconstruction, Validation and Analysis ==
=== March 14 - 17, 2011 ===
-Line 3:
+Line 4:
-Theme - Single particle reconstruction
+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).
-Line 5:
+Line 8:
-||8:00 - 8:50||Registration||Outside PGH 200||
||8:50 - 9:10||Opening remarks/Introduction to Workshop||PGH200||Steve Ludtke and others||
||9:10 - 10:00||[[attachment:1_1_chiu_microscopy.pdf|Introduction to transmission electron microscopy]]||PGH200||Wah Chiu||
||10:00 - 10:50||[[attachment:1_2_henderson_image_processing.pdf|Image Processing Theory]]||PGH200||Richard Henderson||PGH200||
||11:00 - 11:20||Coffee Break||PGH200 Hall||
||11:20 - 12:30||[[attachment:1_3_ludtke_EMAN2.pdf|Tutorial 1 - Getting started with EMAN2, CTF & Class-averages]]||PGH232&200||Steve Ludtke||
||12:30 - 1:30||Lunch||PGH200 Hall||
||1:30 - 3:00||Tutorial 1, contd - Initial models||PGH232&200||Steve Ludtke||
||3:00 - 3:20||Coffee Break||PGH200 Hall||
||3:20 - 5:00||Tutorial 1, contd - First refinement & other issues||PGH232&200||Steve Ludtke||
||5:00 - 6:00||[[attachment:1_4_cong_TriC-CCT.pdf|Research Lecture: Structural studies of TriC/CCT]]||PGH200||Yao Cong||
||6:00 - 9:00||Dinner - with participant short talks||PGH200||
+The data and software required for participation in the tutorial sessions can be found at:
[[Workshop2011]].
-Line 18:
+Line 11:
-Tue Mar 15, 2011
+Information on the location of the workshop and where to park is here: [[Ws2011/Location]]
-Line 20:
+Line 13:
-Theme - Helices & Heterogeneity
+The main workshop page is here: [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_114]]
-Line 22:
+Line 15:
-||9:00 - 10:00||[[attachment:2_1_egelman_IHRSR.pdf|IHRSR]]||PGH200||Ed Egelman||
||10:00 - 10:20||Coffee Break||PGH200 Hall||
||10:20 - 11:20||[[attachment:2_2_penczek_conformation.pdf|Identification of conformational states using resampling]]||PGH200||Pawel Penczek||
||11:30 - 12:30||[[attachment:2_3_goddard_chimera.pdf|Tutorial 2 - Chimera]]||PGH232&200||Tom Goddard||
||12:30 - 1:30||Lunch||PGH200 Hall||
||1:30 - 3:00||[[attachment:2_4_ludtke_EMAN2.pdf|Tutorial 3 - Evaluating refinements, heterogeneity, etc.]]||PGH232&200||Steve Ludtke||
||3:00 - 3:15||Coffee Break||PGH200 Hall||
||3:15 - 5:00||[[attachment:2_5_penczek_SPARX.pdf|Tutorial 4 - Introduction to identification of conformational states in SPARX]]||PGH232&200||Pawel Penczek||
||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||
||6:30 - 9:00||Dinner||Library/Hilton||
+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.
-Line 33:
+Line 18:
-Wed, Mar 16, 2011
+'''Mon Mar 14, 2011'''
-Line 35:
+Line 20:
-Theme - Related methods
+''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]] ||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 ||
||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 ||[[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 || ||
-Line 37:
+Line 34:
-||'''8:50 - 9:15'''||[[attachment:3_1_murray_frealign.pdf|Tutorial 5 - Quick morning tutorial session]]||'''PGH232&200'''||Stephen Murray||
||9:15 - 10:00||[[attachment:3_2_schmid_spt.pdf|Single Particle Tomography]]||PGH200||Mike Schmid||
||10:10 - 10:30||Coffee Break||PGH200 Hall||
||10:30 - 11:00||[[attachment:3_3_lawson_PDB.pdf|EMDatabank.org & Data Archival]]||PGH200||Cathy Lawson||
||11:00 - 11:45||[[attachment:3_4_pintilie_segger.pdf|Tutorial 6 - Segmentation with Segger]]||PGH200&232||Greg Pintilie||
||11:45 - 12:45||Lunch||PGH200 Hall||
||12:45 - 3:00||Tutorial 5 cont'd - Frealign, multirefine, etc.||||PGH200&232||Steve Ludtke & Stephen Murray||
||3:00 - 3:30||Coffee Break||PGH200&232||
||3:30 - 5:00||[[attachment:3_5_montoya_spt.pdf|Tutorial 7 - Single Particle Tomography in EMAN2]]||PGH200&232||Jesus Montoya & John Flanagan||
||5:10 - 6:10||[[attachment:3_6_serysheva_cachannels.pdf|Research Talk - Structural studies of Calcium release channels]]||PGH200&232||Irina Serysheva||
||7:00 - 9:00||Workshop Banquet at Fung’s Kitchen '''Bus leaves U of H at 6:30 !'''||
-Line 49:
+Line 35:
-Thu, Mar 17, 2011
Theme: Validation & Modeling
+'''Tue Mar 15, 2011'''
-Line 52:
+Line 37:
-Morning Lectures (Main lecture hall)
9:00 - 10:00	Richard Henderson
 Validating maps with tilt data
 Resolution
10:00 - 10:30	Break
10:30 - 11:30	Gunnar Schroeder
 DireX
+''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||&do=get]] ||PGH232 ||Dr. Pawel Penczek ||
||11:30 - 12:30 ||[[attachment:2_3_goddard_chimera.pdf|Tutorial 2 - Chimera||&do=get]] ||PGH232&200 ||Tom Goddard ||
||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 || || ||
||3:15 - 5:00 ||[[attachment:2_5_penczek_SPARX.pdf|Tutorial 4 - Introduction to identification of conformational states in SPARX]] ||PGH232&200 ||Dr. Pawel Penczek ||
||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 || ||
-Line 60:
+Line 49:
-Practicals (Computer classroom & Laptops in the lecture hall) 
11:30 - 12:15	Ian Rees
 EMEN2 Tutorial and demo
12:15 - 1:00	Lunch
-Line 65:
+Line 50:
-:00 - 2:30	Yao Cong
 Rosetta Introduction and Tutorial	
2:30 - 3:00	Break
3:00 - 4:30	Matt Baker 
 Gorgon Introduction and Tutorial
+'''Wed, Mar 16, 2011'''
-Line 71:
+Line 52:
-:30 - 5:30	Workshop wrap-up, final issues
+''Theme - Related methods''
||'''8:50 - 9:15''' ||[[attachment:3_1_murray_frealign.pdf|Tutorial 5 - Quick morning tutorial session]] ||'''PGH232&200''' ||Stephen Murray ||
||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||&do=get]] [[attachment:3_3_lawson_EMdepGuide.pdf|Tutorial/Guide]]||PGH232 ||Dr. Cathy Lawson ||
||11:00 - 11:45 ||[[attachment:3_4_pintilie_segger.pdf|Tutorial 6 - Segmentation with Segger||&do=get]] ||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 ||[[attachment:3_5_galaz_spt.pdf|Tutorial 7 - Single Particle Tomography in EMAN2 |&do=get]] ||PGH200&232 ||Jesus Galaz & Dr. John Flanagan ||
||5:10 - 6:10 ||[[attachment:3_6_serysheva_cachannels.pdf|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]]|| ||
-Line 73:
+Line 65:
-workshop ends
+'''Thu, Mar 17, 2011'''
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+Line 67:
-:00 	Speaker dinner
+''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 ||[[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||&do=get]] ||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 || ||

'''''Workshop Ends'''''

''Note: Wah will host a dinner for any speakers who will be around Thurs evening''