The University of Chicago

Jordan Research Group

Computer HowTos

Prepare crystal structure figures

1. Open the cif file with Mercury 3.0. Select Ellipsoid style. In Ellipsoid Settings (menu bar – display – style), check “draw principal ellipses”.

2. If you want to show short contact or H-bond in the structure, check the corresponding boxes in Display Options. Click on the “Contacts…” bottom. In the “Find Contacts” page you can define the contacts (e.g. intermolecular/intramolecular, sum of van der Waals radii plus/minus certain value). In the “Build Network” page you can choose between “expand picked” “delete picked” modes and click on your structure to build the contacts network. You can also delete molecule by right-click on the molecule and choose “Delete this molecule”.

3. If you want to omit all the H atoms but those involved in H-bonding, you can select all H atoms by menu bar – selection – select – select hydrogen. Then click on hydrogen atoms you want to keep to deselect them. Then right-click – Show/Hide – Hide atoms.

4. Change the orientation (hold left bottom), size (right bottom) and position (hold middle bottom) of your structure. When you are satisfied, go to menu bar – File – Save as, choose TIFF file, specify the path and file name, and select a huge size for the image (say 5000 by 5000, make sure the aspect ratio is appropriate for your specific structure). Mecury export TIFF file with 96 dpi resolution.

5. Open the tiff file in GIMP 2.8. Use the Crop tool to remove unnecessary edges. Go to menu bar – Image – Scale Image. Set the resolution to 300 dpi and the width to 8.25 cm (single column for journal). Add atom labels using the Text tool.

6. Export TIFF file. (It seems that compress will not harm the quality of the figure)

Prepare NMR spectra figures

1. Export your NMR spectra from 500-3 or 400-2 to nmr10.
You can create a file named “sync.t”, whose content is
rsync -crv nmr500-3:/opt/topspin/data/username/ /opt/topspin/data/username/
rsync -crv nmr400-2:/opt/topspin/data/username/ /opt/topspin/data/username/
and type “sh sync.t” in the termical should do the work.

2. On nmr10, process your NMR spectra in Topspin. Phasing in NOESY, T1 noise reduction in HOESY can be found here:
http://www.columbia.edu/cu/chemistry/groups/nmr/noesy.pdf

3. In the plotter, manipulate the layout.
http://www.columbia.edu/cu/chemistry/groups/nmr/proton-bruker.pdf
http://www.columbia.edu/cu/chemistry/groups/nmr/HSQC.pdf
These PDFs should answer FAQs, such as how to plot a stacked NMR spectra.

4. Select the spectra, click Edit. You can change the Attributes of the Curve (the 1D, 2D spectra itself), Axes (including the scale) and Grid (usually not displayed).

5. In the pop-up window you can adjust the color, line style, line width, color, font type and size. There are 7 line widths: superthin and 1-6. 3 or 4 seem to be optimum. For the Axes, font type Helvetica and font size between 25-30 pts is recommended. After you make these changes, the spectra would look terrible in the plotter.
Go to menu bar – File – Print – Setup. You can adjust the landscape/portrait and the export image format here (e.g. TIFF). Click OK to bring back to previous window and then click To File. Specify the resolution to be 600 dpi, and click OK. Specify the path and file name in the Selection part. Click OK.
Open your image from the operating system and review it. It looks nicer than in the plotter, but it may not be 100% perfect. Repeat previous steps to improve it.

6. Transfer the image file to your local computer by WinSCP. Edit the Image by GIMP as stated before.

How to Use Pov-Chem and Pov-Ray

In Mercury:

  1. Open your compound of interest.
  2. <Save As…>.
  3. Select <PDB Files (*.pdb *.ent)>.
  4. <OK>.
  5. Create a new folder to hold files in.
  6. Either add or change the file extension of the file to be saved to .pdb.
  7. Save the .pdb file in the new folder.

In Pov-Chem:

  1. <File>.
  2. <Read PDB>.
  3. Select the newly made .pdb file.
  4. <Model>.
  5. <Model Type>.
  6. <CPK>.
  7. Orient the molecule into its final position using the mouse.
  8. <File>.
  9. <Write POV>.
  10. Click the <Write POV> button.
  11. Save .pov file to the same new folder you made which contains the .pdb.

In Pov-Ray: (This may seem like a lot but its not bad at all once you’ve done it)

  1. <Open>.
  2. Select the .pov file.
  3. Toward the top of the code, highlight the two lines of code which start with <right> and press delete.
  4. Toward the middle of the code, in the line starting with <background>, change the three zeros to ones.
  5. Toward the bottom of the code, highlight the line of code which starts with <#warning “> and all lines after and press delete.
  6. Under the <New>, <Open> and <Save> buttons, there is a pull down menu: select <512×384, AA 0.3>.
  7. Click the <Run> button at the top.
  8. If the compound is too close, go to the line of code toward the top: <#declare CameraLocation = < 0, 0, #> ;> and increase the third number in that vector by ca. 5, click <Run> again.
  9. If necessary, repeat using different values until the view of the compound is acceptable.
  10. <Open>.
  11. Select the .ini file from the new folder you created.
  12. At the end of the second line of code, add .bmp.
  13. At the line of code starting with <width>, change the value to 512.
  14. At the line of code starting with <height>, change the value to 384.
  15. <Run>.
  16. A new bitmap picture has been made in the new folder you created containing your compound.

How to Create ORTEPs in XSHELL

Note: ORTEPS may be created using the SHELXTL-XP drawing program by reading either result files (filename.res) or instruction files (filename.ins) generated by the XSHELL program. If you are opening a SHELXTL project using a .res file, be sure that it is the newest .res file (generated from the most current refinement.
The directions below are only meant to provide a quick reference for generating ORTEP drawings. Additional information on more advanced drawing options can be found in the SHELXTL-XP user manual, or by typing help in the XP program.

  1. Enter the SHELXTL program.
  2. Click on the XP option in the top menu of the SHELXTL program.
  3. Type fmol less $Q $H (enter) to generate the atom list (minus all spurious electron density peaks labeled “q” and all hydrogen atoms).
    Note: If hydrogen atoms are to be included, simply type fmol less $Q (enter).
    Alternatively: You may first type fmol (enter). Then type kill $Q (enter). Finally, you may type kill $H (enter).
  4. Type grow (enter) if your molecule resides on a symmetry element in order to generate symmetry related atoms.
  5. Type proj (enter) and view molecule. Use the mouse to click on the keys at the right of the screen to orient the molecule as desired.  When done, click on the exit key.
  6. If necessary, use the kill command to remove undesirable atoms (i.e. you may want to remove solvent molecules from the projection). For example, to remove atom C(1), you would type kill C1 (enter).
  7. If necessary, use undo to delete any incorrect bonds (i.e. undo C1 C2 (enter) will delete the bond between C(1) and C(2).
  8. Type labl 2 500 (enter) to set atom label size.  The default value is 600, but this often appears too large in the final ORTEP projection. For smaller labels, a value of 400 may be used (sets label size to font 8).
  9. ONLY IF you are producing an ORTEP drawing to be used in PowerPoint:
    Type atyp $C 2 14 (enter). This sets the color of all carbon atoms to dark grey, which shows up in PowerPoint as darker than the default value assigned by the SHELXTL-XP program.
  10. Type telp 0 -50 0.030 (enter). The first number refers to the stereo view (0 = mono, -3 = right/left stereo projections, 3 = red/green stereo projection. The second number is the % thermal ellipsoid. The third number is the bond width.  If wider bond widths are desired, the last number may be increased (i.e. telp 0 -50 0.040), or decreased for thinner bonds (telp 0 -50 0.020).  Finally, a fourth number may be added to set the viewer distance.  The fourth number may be useful to reduce the projection size of very large molecules.
  11. Hit enter until the XP prompt asks for a file name, enter a convenient name.
  12. Now use the mouse to orient the label box near the desired atoms.  When you are satisfied with the location of the label box, left click the mouse to label the atom. The current atom that will be labeled is shown at the lower right hand side of the screen.
    Note: The box that appears will often place atom labels over the atoms they are meant to label, therefore, you must use the mouse to place the labels appropriately. Also, space bar will place the labels where the box is located, while the enter key allows you to skip over an atom without labeling it.
  13. When done labeling atoms, hit enter to return to XP prompt. Next, type draw followed by the filename you entered in step 9, then enter. A series of choices for output file type, filename, color/black and white, and paper size will follow.
    1. For creating ORTEP files for use in PowerPoint, type a (enter) for adobe postscript format. For creating files for use in Microsoft Word, type h (enter) for hpgl file format.
    2. Type in a convenient filename when prompted, then enter.
    3. Choose c (enter) for color ORTEP, or simply hit enter for black and white  ORTEP (default).  If color ORTEP is chosen, there will be a pause after typing c (enter), so be patient.  Also, ignore step iv. if color ORTEP is chosen.
    4. Hit enter (choose default) for paper size.
  14. Type exit to leave program.

Note: The ORTEP you have created will be deposited in the folder from which you opened the .res or .ins file.

PowerPoint With Chime

Updated: Spring 2004.

The PPTWC package was assembled to allow the use of interactive and animated three dimensional models during a power point presentation.

The “LiveWeb” Add-In embeds Microsoft Internet Explorer inside of Power Point. The Chime plug-in is used to render Three dimensional structures in real time via a web page. The combination of these two utilities allows for the unique ability to have interactive spacefilling and ball and stick models.

Before proceding you must have the PPTWC file set, which includes:

  • “LiveWeb” Power Point Add-In by Shyam Pillai.
  • MDL Chime plugin.
  • Default view files (ball and Stick: ballstick.html; spacefill: spacefill.html; ball and stick rotate: ballstickrotate.html; spacefill rotate spacefill: rotate.html)

Install the MDL Chime browser plug-in

double click on MDLChimeSP6.exe and follow the instructions.

Install the LiveWeb Add-In

  1. Proper file format
    All structures viewed in chime must first be in the brookehaven protein data bank format or .PDB This is a generic format that is supported by almost all structural viewing and computational software.
  2. View the PDB file with chime
    Two options available:
    • View the PDB file without any formatting options. This will display the wireframe structure on a black background. To do this, right click on the PDB file select open with and select Internet explorer.
    • View the structure using a prepared HTML file with preselected formatting options.(*)
    1. Right click on the HTML file with the settings you intend to use.
    2. Select copy and then paste.
    3. Rename the duplicate HTML file using a unique filename (example: SMK-155.html).
    4. Open the HTML file using notepad (do this by using the same open with options explained above).
    5. Change the 7th line of the HTML file so that your filename is in place of the highlighted text. When you are done it should read:
      embed src=”yourPDBfilename.PDB” align=abscenter width=100% height=100%
    6. Select the file menu and choose save.
    7. Double click your HTML file to open it with Internet explorer.

Change the “default view” of your PDB file

When IE opens a PDB file using the Chime plug-in the orientation of the model is along the Z axis. This is not necessarily the view that you will want in your power point slide.  To change the orientation of the model when you load the PDB file.

  1. Open your HTML file that you created in part (*).
  2. Rotate your structure using the mouse until it is in the orientation you desire.
  3. Right click on the chime structure and select Edit, Copy chime script.
  4. Create a piece of electronic scratch paper, right click on your desktop and select New, Text Document.
  5. Select edit, paste.
  6. The information you have pasted into the text file is the script to generate the orientation you selected.
  7. The rotation information  is near the top of the file and looks like
    reset
    slab off
    rotate z -79
    rotate y -10
    rotate x -153
    zoom 190
  8. The z, y and x coordinates should then be entered into your HTML file. When you are done your code should look like,
    set ambient 30; rotate z -3; rotate y -34; rotate x -85; zoom 190″>
    with your rotational parameters in the highlighted region.
  9. Save the HTML file by selecting File, Save.
  10. Open your HTML file in IE to make sure that it looks the way you would like.
  11. Tweak the zoom value until you are satisfied with the image.
  12. You can delete your “electronic scratch paper” now if you would like.
  13.  

Change the animation controls

The Chime plug-in has the capacity to automatically rotate the model when a button is clicked.  The commands for the rotation button are already included in the   ballstickrotate.html and spacefillrotate.html files. The default animation is to rotate the molecule 2 whole times (720 degrees) in 27 seconds. The script for the rotation button is.

script=”move 0 720 0 0 0 0 0 0 27″

The first three numbers correspond to x-axis rotation, y-axis rotation and z-axis rotation. The last number corresponds to the total time the animation should take. The other numbers are for more advanced types of animation.

Be sure to try out your new animation before using it in a slide show.

Embed your chime image / animation into powerpoint

Make sure that both your HTML file and your PDB file are in the C:\PPTWC\ directory. This directory and file structure MUST be maintained throughout the ENTIRE GROUP so that when other members (including Prof. Jordan) need to use your chime slides there will be no unexpected complications.

Open your Power Point presentation and Select Insert, Web Pages.. and follow the instructions when asked for a URL, enter C:\PPTWC\”uniquefilename.html” where “uniquefilename” is your HTML filename.

The web page will be inserted as a large windows logo and can be resized and manipulated like any other picture or power point object.  The Chime image can only be viewed during the slide show mode.

Once you have resized and formatted the slide to your likeing make sure that you double check the way everything looks in the slide show.