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C:\Documents and Settings\Pete\My Documents\Archives\Graduate Files (Revised 8/27/08) Introduction to Molecular Modeling Lab 2 - Modeling Input files Table of Contents Objectives .........................................................................3 Setting up..........................................................................3 Remote Access to Amber, Frodo, and Iris ...........................................3 From a PC .............................................................3 From a Unix Workstation .................................................4 Obtaining Protein and Oligonucleotide Structures ..........................................5 Directory setup................................................................5 Mozilla ......................................................................6 PC....................................................................6 Unix Machine ..........................................................6 Protein crystal structure files.....................................................6 Oligonucleotide crystal structure files ..............................................7 FTP file transfer...............................................................7 Unix to Unix ...........................................................7 PC to Unix.............................................................9 Structure data & searching (coordinate files) ........................................9 Viewing .pdb files ..................................................................10 Protein .pdb file structure .......................................................10 Resources for processing files - File format conversion ...............................12 Viewing with rasmol..........................................................12 Unix Machine (e.g. Amber, Iris, or Frodo) ...................................12 On a PC..............................................................13 Viewing .pdb files with Moilview ................................................14 Other programs for visualizing structure files.......................................14 Image Databases .......................................................14 Processed Image viewers and Editors.......................................14 Basic Model Visualization Tools and Plug-ins................................14 OnLine Structure Visualization (Java/VRML-compliant Web Browser)............15 xleap - Setting up for Molecular Mechanics and Molecular Dynamics .........................15 The Universe Editor...........................................................15 The Unit Editor ..............................................................16 The Parameter Editing Table....................................................17 Viewing the protein and oligonucleotide structures ..................................17 Printing Structures..................................................................18 Printing from a PC............................................................18 Rasmol...............................................................18 Other PC programs .....................................................18 Printing in the Molecular Modeling lab............................................18 Rasmol...............................................................18 Moilview .............................................................19 Exercises .........................................................................19 3 Objectives The objectives of this lab are to learn 1) how to locate the structures of proteins or oligonucleotides from web sources for molecular modeling, 2) down load structure to the workstation, 3) modify the file if necessary, 4) display it, and modify if desired. 5) Print your pictures. This laboratory will require you to use the skills you learned in the first lab (Unix tutorial). If you did not complete that tutorial, you may have some difficulty with this laboratory. It would be a good idea to complete the tutorial. At a minimum, you should have the Unix tutorial lab handout as you work through this lab. The flow of this lab will be as follows: 1) Set up your user account so that the required programs will be available to you. 2) Use netscape to browse protein and nucleic acid data bases for desired structures. 3) Retreive a protein and an oligonucleotide structure. 4) Run viewing programs to inspect the structures retrieved. 5) Print pictures (files). Setting up Remote Access to Amber, Frodo, and Iris From a PC: General instructions for remote access to to the lab computers have been given in lab 1 and should be followed here. There are some additional considerations that need to be pointed out. Here, some of the hardware and software you will find useful will be listed. Some of the software is freely available, some will have to be purchased, depending upon what you want to do and how reasonable it might be to come to the lab. 1) Hardware. Assuming you have a PC and an internet connection, there are only two pieces of hardware you might need. First, a three button mouse is almost a must. Amber (specifically xleap), Sybyl and InsightII use a three button mouse for manipulating structures. If you do not have a three button mouse, 4 you ability to manipulate structures on the screen will be severely limited and it is strongly advised that you get one. Scrolling mice (the kind with the wheel/button) usually work (though sometimes they behave oddly) as well as mice with three buttons though the latter are slightly more convenient to use here. Second, while more of a luxury than a requirement, a color printer is very useful for printing structures. A B/W printer is sufficient for simple structures, but for more complicated ones, color really helps. 2) PC Software: A few programs that will help you are rasmol (and or Weblabviewer Lite), a good FTP program (I recommend WS_FTP_LE for non-secure FTP, WINSCP for secure shell FTP), and a plotting program (I use either Sigma-Plot or Psi-plot. Any plotting program that can import ASCII files will work. For the PC savvy, you can download GRACE. The equivalent of this program, xmgr, is used on the Unix machines, Grace on the Linux machines in the modeling lab. Note that xmgr and Grace are really the same program by different names) rasmol or better pymol (and there are PC, Mac, Linux, and Unix versions are available) and Weblabviewer Lite can be downloaded at no cost. The Websites are given below. Likewise, WS_FTP95 can be downloaded at no cost. If you find a good plotting program for a PC that is free, let me know. rasmol http://www.umass.edu/microbio/rasmol/getras.htm Pymol http://pymol.sourceforge.net/ Viewer Comparison http://pymol.sourceforge.net/pmimag/compare.html (this site compares Pymol, Rasmol, MolMol, VMD, Chimera, DeepView, and Python, gOpenMol, Qmol, Biodesigner) WS_FTP9_LE http://www.ftpplanet.com/download.asp WINSCP http://winscp.net/eng/download.php Some of the machines in the modeling lab require your computer to be running secure-shell. Below are sites from which secure-shell software can be obtained, at now cost, and for any operating system. PuTTY http://www.chiark.greenend.org.uk/~sgtatham/putty/ OpenSSH http://www.openssh.com/portable.html#http (This site has a list of mirror sites from which OpenSSH can be downloaded.) All of these programs are self-executing and will set themselves up when you run them. From a Unix Workstation 1) Login to you account on any of the three SGI computers and edit your .cshrc file. Add the following line to the end of this file using the text editor of your choice (eg nedit, jot, vi). You must do this on each machine you have an account on otherwise many of the programs will not work as describe in this and subsequent labs. Basically, this will set up you user environment so that you have access to the programs you need on each machine. It will also set up some aliases to make it easier to telnet and ftp between machines. 5 source /usr/local/amberr or source /disk02/usr/local/amberr depending upon which machine you areon. After you have editted your .cshrc file, enter the command shown below. source .cshrc This is the only time you will have to enter this command as each time you login in this will be done for you. Obtaining Protein and Oligonucleotide Structures The input files you might want or need for many proteins and oligonucleotides can be obtained for databases you can access via the internet. It is not the purpose of this lab to explore all of these databases. Instead, one database for proteins and one for nucleic acids will be used to introduce you to what is available and to obtain a protein and an oligonucleotide structure. At the end of this section are web addresses for databases containing protein and oligonucleotide crystallographic information in addition to those used here. Another source is on the Computational Chemistry and Molecular Modeling Lab’s homepage - links (http://www.hsc.wvu.edu/sop/compchem/links.htm). Directory setup Prior to starting any project, it is good practice to set up a directory or directories to do your work in and to keep all the relevant files together. For this lab you will need to set up two directories. 1) Create the following subdirectories to put your work in. Type the following two commands: mkdir ~/protein_data (~/ refers to your home directory, where you are when you login. If you are in your home directory, simply entering mkdir protein_data will work just as well.) mkdir ~/dna_data 2) Change to the ~/protein_data directory: cd ~/protein_data 6 Mozilla PC If you are running from a PC, you must use your
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