Skip to content

Commit

Permalink
Update index.md new schedule
Browse files Browse the repository at this point in the history
  • Loading branch information
@spindrj
spindrj authored Dec 31, 2023
1 parent 56a51e6 commit 71ed808
Showing 1 changed file with 90 additions and 97 deletions.
187 changes: 90 additions & 97 deletions courses/methods_2023/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ This is a team-based class where students work in small groups develop their own

*Commitment to Diversity, Equity and Inclusion*: The course instructors and teaching assistants value the contributions, ideas and perspective of all students. It is our intent that students from diverse backgrounds be well-served by this course, that students' learning needs be addressed both in and out of class, and that the diversity that the students bring to this class be viewed as a resource, strength and benefit. It is our intent to present materials and activities that are respectful of diversity: gender identity, sexuality, disability, age, socioeconomic status, ethnicity, race, nationality, religion, and culture. However, we also acknowledge that many of the literature examples used in this course were authored in an environment that marginalized many groups. Integrating a diverse set of experiences is important for a more comprehensive understanding of science and we strive towards that goal. Although the instructors are committed to continuous improvement of our practices and our learning environment, we value input from students and your suggestions are encouraged and appreciated. Please let the course director or program leadership know ways to improve the effectiveness of the course for you personally, or for other students or student groups. (modeled after CCB and [Brown University's Diversity & Inclusion Syllabus Statements](https://www.brown.edu/sheridan/teaching-learning-resources/inclusive-teaching/statements))

## 2022 schedule
## 2023 schedule

## TEAM ASSIGNMENTS

Expand Down Expand Up @@ -85,11 +85,22 @@ This is a team-based class where students work in small groups develop their own
- Tracy Lou
- David Larwood

# Jan 9-11 - Class intro
# Jan 8-10 - Class intro

## Monday January 9
- Welcome: structure of the class, zoom vs. in person norms, teams and work-together recommendations, auditing, relationship to Macro mini-quals, final writeups for this class (JF)
- [FFT 101](https://docs.google.com/presentation/d/13-tG0L3H70MA232TBcsvv3pkHsm3K2sVot4vDs9Xl5E/edit#slide=id.g10a62644d57_1_0) (JF)
## Monday January 8
- Welcome: structure of the class, teams and work-together recommendations, auditing, relationship to Macro mini-quals, final writeups for this class (AM)
- Why structural biology (AM)
- High-level review of thermodynamics and kinetics (JDG)
- [Forces contributing to the conformational stability of proteins](https://faseb.onlinelibrary.wiley.com/doi/pdfdirect/10.1096/fasebj.10.1.8566551)

- The technique in a few minutes with reference to the importance of the Fourier Transform!
- AM Xray crystallography
- KV CryoEM
- JG NMR


## Tuesday January 10
- [FFT 101](https://docs.google.com/presentation/d/13-tG0L3H70MA232TBcsvv3pkHsm3K2sVot4vDs9Xl5E/edit#slide=id.g10a62644d57_1_0) (AM, JDG, KV)
- Waves: amplitude/intensity, phase, frequency/wavelength (and in multiple dimensions: direction/index)
- How to sum sine waves together: weights/amplitude - can make any periodic function!
- Intuitively decomposing a complex function into sine waves (Fourier transform!)
Expand All @@ -98,24 +109,7 @@ This is a team-based class where students work in small groups develop their own
- [interactive website used in class for demo](http://www.jezzamon.com/fourier/)
- [sin wave grapher](https://www.desmos.com/calculator/w9jrdpvsmk)
- [another cool fourier thing](https://www.tomasboril.cz/fourierseries3d/en/)
- The technique in a few minutes with reference to the importance of the Fourier Transform!
- JF Xray crystallography
- KV CryoEM
- JG NMR

## Tuesday January 10

- Followups from first class:
- [Fourier Transform from Grant Jensen](https://www.youtube.com/playlist?list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-), especially videos 14-19, focusing on the 2D and 3D Fourier Tranform ones!
- [Andrea Thorn intro to Crystallography series](https://www.youtube.com/watch?v=mDbmfyOGLIM&list=PLHHBmgJ8vFm6xZPlWlRGuBaoOM3OGlN5T) - especially video 4 on the Fourier Tranform and minute 37 of that video on Franklin's photograph
- [Cynthia Wolberger on Franklin](https://www.youtube.com/watch?v=62BYOReS7BU)
- [a longer video on Franklin featuring Cynthia Wolberger](https://www.mskcc.org/videos/kravis-wise-life-and-legacy-dr-rosalind-franklin-november-23-2020)

- Why structural biology/Intro to Pchem (JG)
- [Forces contributing to the conformational stability of proteins](https://faseb.onlinelibrary.wiley.com/doi/pdfdirect/10.1096/fasebj.10.1.8566551)


- BEAMLINE trip Feb 16th

- software check:
- coot
- phenix
Expand All @@ -124,125 +118,82 @@ This is a team-based class where students work in small groups develop their own
- pymol
- EMAN2
- NMRBox signup
- Additional Material, this could be deleted
- [Fourier Transform from Grant Jensen](https://www.youtube.com/playlist?list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-), especially videos 14-19, focusing on the 2D and 3D Fourier Tranform ones!
- [Andrea Thorn intro to Crystallography series](https://www.youtube.com/watch?v=mDbmfyOGLIM&list=PLHHBmgJ8vFm6xZPlWlRGuBaoOM3OGlN5T) - especially video 4 on the Fourier Transform and minute 37 of that video on Franklin's photograph
- [Cynthia Wolberger on Franklin](https://www.youtube.com/watch?v=62BYOReS7BU)
- [a longer video on Franklin featuring Cynthia Wolberger](https://www.mskcc.org/videos/kravis-wise-life-and-legacy-dr-rosalind-franklin-november-23-2020)


- TEAM 1 to negative stain with KV

## Wednesday January 11

## Wednesday January 10
- [ChimeraX tutorial by Tom Goddard](https://www.rbvi.ucsf.edu/chimerax/data/stanford-apr2022/cryoem_intro.html)
- Some past tutorials:
- [Color by Chemical Shift Perturbations](https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/chemshift.html)
- [How to View Nanobody Molecular Dynamics in ChimeraX](https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/nanobody_md.html)


# Jan 17-24 - CryoEM - Lectures Yifan Cheng, Tutorials Klim Verba
# Jan 16-24 - CryoEM - Lectures Yifan Cheng, Tutorials Klim Verba

## Monday January 16
## Monday January 15
MLK DAY - HOLIDAY

## Tuesday January 17
## Tuesday January 16
### [9-11: Lecture 1 from Yifan Cheng](https://ucsf.box.com/s/8319vx3dci0gr5r33ge2y9am67fuzuoq)

## Wednesday January 18
## Wednesday January 17
### [Key questions to track understanding of CryoEM](https://docs.google.com/document/d/1swcAbr6AHVkPFQyuqr0sYSLOwMbF1G3zGRfvRY6O2zE/edit)
### [9-10: Lecture 2 from Yifan Cheng](https://ucsf.box.com/s/8319vx3dci0gr5r33ge2y9am67fuzuoq)
### 10-11: Intro to data processing by TAs after short intro by KV
- TEAM 2 to negative stain with KV?
- other teams work on data processing tutorial with TAs

## Thursday January 19
## Thursday January 18
- TEAM 3 to negative stain with KV (outside of class time)

## Monday January 23
## Monday January 22
- TEAM 4 to negative stain with KV
- Cryo show and tell, teams 1 and 2
- other teams work on data processing when not at microscope

## Tuesday January 24
## Tuesday January 23
- Cryo show and tell, teams 3 and 4
- other teams work on data processing when not at microscope
- rigor and reproducibility - lecture by Klim Verba

- ## Wednesday January 24
Cryo show and tell, team 5
- other teams work on data processing when not at microscope
-
## Reading on rigor and reproducibility in EM:
- [cisTEM paper](http://cdn.fraserlab.com/courses/methods/2018_grant.pdf)
- [FSC](https://en.wikipedia.org/wiki/Fourier_shell_correlation) and [early example in EM](http://cdn.fraserlab.com/courses/methods/1982_saxton.pdf)
- [half maps](http://cdn.fraserlab.com/courses/methods/2012_scheres.pdf) and [Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy](http://cdn.fraserlab.com/courses/methods/2003_rosenthal.pdf)
- Other Model and Map validation tools (a lot of overlap with X-ray tools but a few examples that don't: [phenix.mtriage](https://www.phenix-online.org/documentation/reference/mtriage.html), [EMRinger](http://cdn.fraserlab.com/publications/2015_barad.pdf))

# Jan 25-Feb 6 - NMR - Lectures John Gross

## Wednesday January 25
### [Lecture 1 from John Gross, Introduction to Multidimensional NMR](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE1.pdf)
- intro to the system (nanobodies)
- demonstration of NMR data processing, John Gross
- [from FID to 2D](http://cdn.fraserlab.com/courses/2022_2DNMR_Processing_Tutorial.pdf) (Allie Born and John Gross)
- Supplemental reading: [How does an HSQC work?](http://cdn.fraserlab.com/courses/methods/HSQC-Guided-tour.pdf)

## Monday January 30
### [Lecture 2 from John Gross, Detecting Ligand and Protein Interactions by NMR](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE2.pdf)
- process 15N HSQC and 13C HSQC data with teams (Allie Born and John Gross)

## Tuesday January 31
### [Lecture 3 from John Gross, Dynamic NMR -Hydrogen Deuterium Exchange (HDX) and intro to ms-usec dynamics](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE3.pdf)
- Overlay Nb6:Spike RBD complexes with Nb6 in CcpNMR, demo by Allie Born (Allie Born and John Gross)
- [CcpNMR tutorial](http://cdn.fraserlab.com/courses/ccpNMR_Tutorial.pdf)
- As an alternative to CcpNMR, you may use [Sparky tutorial](http://cdn.fraserlab.com/courses/2022_Sparky_tutorial.pdf)
- Supplemental reading: [CSP mapping by NMR when resonance asignments of the bound state are unknown](http://cdn.fraserlab.com/courses/methods/1996_farmer.pdf)

## Wednesday Feb 1
### [Lecture 4 from John Gross, Methods to quantify slow dynamics, ZZ-exchange and CPMG](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE4.pdf)
## Monday Feb 6
### Lecture 5 from John Gross, Measuring ns-ps dynamics in proteins
- process mNb6:RBD 15N and 13C HSQC spectra, overlay with mNb6. Cross-peak bookkeeping with teams (Allie Born and John Gross)

## How to setup and process HSQCs on the 800 MHz spectrometer
- [Acquiring_2D_15N-HSQC_in_TopSpin](https://ucsf.box.com/s/tc0dg14opvz3bfdht92r6pn56h3i7fg4)
- [Processing_Data_in_TopSpin](https://ucsf.box.com/s/6jznx75m14b24xf84ot8cgporudfkf8i)
- [Topspin_Commands](https://ucsf.box.com/s/7gss7koit3a9v0iccm0arukojzkf8u9l)

## Materials for TA Office Hours
- [1-an example 13C HSQC of Nb6 , 2-Nb6 and mNb sequences, 3-Sparky tutorial](https://ucsf.box.com/s/boxmdnws7xbg04p812agth005b7augu5)

## Reading on rigor and reproducibility in NMR:
- [Tools for validating NMR structures](http://cdn.fraserlab.com/courses/methods/2014_vuister.pdf)
- [Q-scores](http://cdn.fraserlab.com/courses/methods/2004_clore.pdf)
- [Integrative modeling](http://cdn.fraserlab.com/courses/methods/2019_rout.pdf)

# Feb 7-8 - Computational Approaches and Community Building in Structural Biology

## Tuesday February 7
### Lecture from Tanja Kortemme - AlphaFold and RosettaFold
# Jan 29-Feb 7 X-ray Crystallography - Lectures Bob Stroud, Tutorials Aashish Manglik

## Wednesday February 8
### Lecture from Lisa Eshun-Wilson - Her recent structural biology work and building Diversity, Equity, and Inclusion in structural biology
- Reminder to [install crystallography software!](https://docs.google.com/document/d/1pRA-pERFvX05yrGZcZjfugxiV5YDyrFsX64yHhcyOmw/edit#)
- Last check for beamline trips logistics

# Feb 13-22 X-ray Crystallography - Lectures Bob Stroud, Tutorials James Fraser
## Monday February 13
## Monday January 29th
### 9-1030: Lecture 1 from Bob Stroud
### 10:30-11: [Tutorial 1: What's the deal with the spots](https://docs.google.com/document/d/1X3tadTbEAufeBVTrYBy6r9d9Tl5dael7KQTJv6_4ACA/)
- What is the system?
- Examine diffraction data in adxv
- ### [Beamline trip logistics](https://docs.google.com/document/d/15U3DUiw0-ZLWWhC4zfXiKAnn0G1odUyRf1RXIWibkM0/edit?usp=sharing)

## Tuesday February 14
## Tuesday January 30th-BEAMLINE TRIP!!!
## Wednesday January 31st-BEAMLINE TRIP!!!

## Monday February 5
### 9-10:30: Lecture 2 from Bob Stroud
### 10:30-11: [Tutorial 2: Data Reduction](https://docs.google.com/document/d/1X3tadTbEAufeBVTrYBy6r9d9Tl5dael7KQTJv6_4ACA/edit#bookmark=kix.if962aravtol)
- Use xia2 to process diffraction data
- Understand various metrics for data reduction
- What do we have at the end? MTZ files!
- [XRayView Download](https://www.phillipslab.org/downloads)

## Wednesday February 15
## Tuesday February 6
### 9-10:30: Lecture 3 from Bob Stroud
### 10:30-11:30: Facility tour with [Violla Bassim](mailto:[email protected])

## Thursday February 16 - BEAMLINE TRIP!!!

## Monday February 20 - PRESIDENTS DAY

## Tuesday February 21

### [Tutorial 3: Molecular Replacement](https://docs.google.com/document/d/1X3tadTbEAufeBVTrYBy6r9d9Tl5dael7KQTJv6_4ACA/edit#bookmark=id.snbyu3mveba6)

### [Tutorial 4: Model Refinement](https://docs.google.com/document/d/1X3tadTbEAufeBVTrYBy6r9d9Tl5dael7KQTJv6_4ACA/edit#bookmark=id.m85sdq3icnmn)
Expand Down Expand Up @@ -276,18 +227,60 @@ MLK DAY - HOLIDAY
- A/B conformations
- mutually exclusive


## Wednesday February 22

## Wednesday February 7
### 9-10:30: Lecture 4 from Bob Stroud
### Continue Model Refinement and [Tutorial 5: Model Analysis](https://docs.google.com/document/d/1X3tadTbEAufeBVTrYBy6r9d9Tl5dael7KQTJv6_4ACA/edit#bookmark=kix.z40bd2t29nx4)

## Reading on rigor and reproducibility in Crystallography:
- [R-free](http://cdn.fraserlab.com/courses/methods/1992_brunger.pdf)
- [MolProbity](http://cdn.fraserlab.com/courses/methods/2010_chen.pdf)
- [Data Challenges and synthetic data](http://cdn.fraserlab.com/courses/methods/2019_holton.pdf)
- [Protein crystallography for non‐crystallographers, or how to get the best (but not more) from published macromolecular structures](https://febs.onlinelibrary.wiley.com/doi/full/10.1111/j.1742-4658.2007.06178.x)

# Final write up due: one per team - Feb 27
# Feb 12-Feb 21 NMR - Lectures John Gross, Tutorials Amy Guo and Catherine Kuhn
## Monday February 12
### [Lecture 1 from John Gross, Introduction to Multidimensional NMR](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE1.pdf)
- intro to the system (nanobodies)
- demonstration of NMR data processing, John Gross
- [from FID to 2D](http://cdn.fraserlab.com/courses/2022_2DNMR_Processing_Tutorial.pdf) (Allie Born and John Gross)
- Supplemental reading: [How does an HSQC work?](http://cdn.fraserlab.com/courses/methods/HSQC-Guided-tour.pdf)

## Tuesday February 13
### [Lecture 2 from John Gross, Detecting Ligand and Protein Interactions by NMR](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE2.pdf)
- process 15N HSQC and 13C HSQC data with teams (Allie Born and John Gross)

## Wednesday February 14
### [Lecture 3 from John Gross, Dynamic NMR -Hydrogen Deuterium Exchange (HDX) and intro to ms-usec dynamics](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE3.pdf)
- Overlay Nb6:Spike RBD complexes with Nb6 in CcpNMR, demo by Allie Born (Allie Born and John Gross)
- [CcpNMR tutorial](http://cdn.fraserlab.com/courses/ccpNMR_Tutorial.pdf)
- As an alternative to CcpNMR, you may use [Sparky tutorial](http://cdn.fraserlab.com/courses/2022_Sparky_tutorial.pdf)
- Supplemental reading: [CSP mapping by NMR when resonance asignments of the bound state are unknown](http://cdn.fraserlab.com/courses/methods/1996_farmer.pdf)

## Monday February 19
Presidents Day - HOLIDAY

## Tuesday February 20
### [Lecture 4 from John Gross, Methods to quantify slow dynamics, ZZ-exchange and CPMG](http://cdn.fraserlab.com/courses/Methods-NMR-2022-LECTURE4.pdf)

## Wednesday February 21
### Lecture 5 from John Gross, Measuring ns-ps dynamics in proteins
- process mNb6:RBD 15N and 13C HSQC spectra, overlay with mNb6. Cross-peak bookkeeping with teams (Allie Born and John Gross)

## How to setup and process HSQCs on the 800 MHz spectrometer
- [Acquiring_2D_15N-HSQC_in_TopSpin](https://ucsf.box.com/s/tc0dg14opvz3bfdht92r6pn56h3i7fg4)
- [Processing_Data_in_TopSpin](https://ucsf.box.com/s/6jznx75m14b24xf84ot8cgporudfkf8i)
- [Topspin_Commands](https://ucsf.box.com/s/7gss7koit3a9v0iccm0arukojzkf8u9l)

## Materials for TA Office Hours
- [1-an example 13C HSQC of Nb6 , 2-Nb6 and mNb sequences, 3-Sparky tutorial](https://ucsf.box.com/s/boxmdnws7xbg04p812agth005b7augu5)

## Reading on rigor and reproducibility in NMR:
- [Tools for validating NMR structures](http://cdn.fraserlab.com/courses/methods/2014_vuister.pdf)
- [Q-scores](http://cdn.fraserlab.com/courses/methods/2004_clore.pdf)
- [Integrative modeling](http://cdn.fraserlab.com/courses/methods/2019_rout.pdf)



# Final write up due: one per team - Feb 26
- EM: which of the 12 sequences/structure is your sample? Explain how you processed your data and identified which one it is? How can you quantify whether you are correct?
- Piezo1
- Spliceosome
Expand Down

0 comments on commit 71ed808

Please sign in to comment.