2017 NMRFAM Advanced Structure Refinement Workshop
Sunday, August 6th, 2017 – Wednesday, August 9th, 2017 (CANCELLED)
Scope. A hands-on workshop: Vignettes on the use of various restraint types in NMR structure determination.
A series of lectures and hands-on use of Xplor-NIH for the determination and refinement of NMR based structures.
1 – Xplor-NIH introduction and overview
2 – Basic structure calculations
3 – Generation of structures for a toy peptide
4 – NOE distance & dihedral angle restraints
5 – Structure calculation and evaluation of results
6 – Refinement (RDC, PRE, SAXS,…)
7 – Complexes (Protein, Nucleic acid, small ligand)
8 – Validation/deposition
1 – XPLOR-NIH / Python
2 – Pymol
3 – MolProbity
4 – Linux platform – VNC
Format.Each section will begin with a short lecture followed by a hands on session in which participants will be given time to perform each step of protein structure determination using data provided by NMRFAM. The staff will be available throughout the workshop sessions as a resource to assist participants and answer questions.
Participant Requirements.The workshop will be using XPLOR-NIH and related software that is installed on a NMRFAM linux compute server. VNC will be use to access the servers. Knowledge of Linux is not required but it would be very useful for the linux novice to peruse some of the many linux introductions found online, which include both documents and videos. A basic level of understanding of the methods used in NMR structure determination (e.g. assignments, NOE restraints) will be assumed. All data used in the workshop will be provided.
All participants will be installing a Virtual machine (VM) on their laptop. A VM is an emulation of a particular computer system that can be installed and run on all flavors of other operating systems. We are using a VM that runs the linux operating system Ubuntu 14.04. To run this on your computer, you will need to install VirtualBox (Oracle), which is freely available at www.virtualbox.org. Oracle VirtualBox is a virtualization software package for x86 and AM64/Intel64-based computers. Supported host operating systems include Mac OS X, Windows XP, Windows Vista, Windows 7 and Windows 8, among others. In order to install VirtualBox, you MUST have administrative privileges on your computer. For PCs, VirtualBox requires the enabling of virtualization in the BIOS. For Macs, the capability of reading a NTFS formatted flash drive is required. The required open source software packages are: FUSE for Mac OS X (http://osxfuse.github.io/) and NTFS-3g for Mac OS X (http://sourceforge.net/projects/catacombae/files). It is recommended that to run the workshop software on VM, the computer used should have 4GB of memory and a 64 bit computer. The memory and bit size are not strict requirements, but the speed will suffer and make the workshop rather painful. The computer should have >15GB of free disk space. A mouse is recommended. Testing of the VirtualBox Installation can be done by using the (very small-54MB) linux VM located on our ftp site. To download the VM: Copy and paste the following link ftp://login1.nmrfam.wisc.edu/pub/nmrfam/ into your browser and click on VM_test.ova. Once VirtualBox has been installed, doubleclick on the VM_test.ova file and then click on “import” in the window that appears. Once that has finished click on “start” with VM_test highlighted. The desktop of a SliTaz GNU/Linux VM should appear. This is a (remarkably small) usable linux computer, but it is NOT the VM that will be use in the workshop. The size of the workshop VM is ~7GB and takes longer to download and install, thus the test VM is used to assure the correct installation of VirtualBox.
Each participant is required to bring in their own laptop computer (with either wireless capability or preferably, a wired ethernet port) to the workshop. We also recommend that participants bring a mouse for their laptop.
Schedule and Important Dates.
Monday, July 10, 2017 – Last day to obtain lodging at Wisconsin Union Hotel
Thursday, July 20, 2017 – Last day to obtain lodging at Adams Residence Hall
Monday, July 31, 2017- Last day to register for the workshop
Thursday, August 3, 2017 – Last day to obtain lodging at Best Western InnTowner
Sunday, August 6, 2017 (2:30pm) – Workshop Opening Reception/Computer Set-up (ATTENDANCE REQUIRED)
Monday to Tuesday, August 7-8, 2017, Full days of workshop. Barbecue dinner on 8th at 6pm.
Wednesday, August 9, 2017 – 3:30pm – Workshop ends.
Registration. The fee for the workshop will be $350 and includes all materials necessary to participate in the workshop and includes the opening reception, barbecue dinner on August 8th as well as the morning and afternoon refreshments. The registration fee does not include your lodging/housing or parking costs (see below for more information). Complete the 2017 Advanced NMRFAM Structure Refinement Workshop Registration form. Make the payment via credit card or check as detailed in the registration form. Send your registration form to Lai Bergeman via e-mail. Note: registration for the workshop closes on July 31st, 2017
Parking. visit UW Madison’s Transportation services website, e-mail them or call them a 608-262-8683 during normal businesshours between 8:30am and 4:15pm CST, Monday through Friday.
Lodging. Travel and lodging are to be arranged and paid for separately by each participant. There are 3 options for lodging:
1. Best Western InnTowner located at 2424 University Ave. Please use the group code “NMRADV“. The rate at $92/night as single/double occupancy The last date for room reservation is August 3rd, 2017. Rates include complimentary parking, free WIFI, free airport and campus shuttle to workshop, and a complimentary breakfast. Reservations can be made online or call 608-233-8778.
2. Adams Residence Hall located at 1520 Tripp Circle, Please use the group code “NMRFAM ADVANCED” to make your reservation. The rate is $29/night for single occupancy only. The last date for room reservation is July 20th, 2017. Reservations can be made online (link will be established by Wednesday, March 1st). For questions, please contact the Housing Conference Services offices at 608-262-5576 or email.
3. Wisconsin Union Hotel located at 1308 W. Dayton St. Please use group code “NMRADV” to make your reservation. The rate is $161/night. One parking space is included under the hotel with each room reservation. The last date for room reservation is July 10th, 2017. Reservations can be made online or call 608-263-2600.
If you have any questions about the workshop and how to register, e-mail Lai Bergeman or call 608-262-3173.
We hope that you can participate in this third Advanced workshop and become part of our NMRFAM user!