PYMOL FAQ

 

 

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    How can I show electron density?

    Pymol can read several map formats, but not mtz files. You must create a map. A map created by ccp4 must have the extension .ccp4 (2f.ccp4, etc.) To create a map from an mtz file, use the Run FFT - Create Map task in ccp4i. If you have created the mtz file using refmac in ccp4i, you can use the task Create Task-Specific Maps. Both of these are found under the Map & Mask Utilities pulldown. Check in coot that the map is sane.

    Read in the map, then use an isomesh command to create a density object

    isomesh try1, overa, 1.1, (sel01), 3., 1,2

    where try1 is the object name, overa the map name, 1.1 the contour level, selection, the region of the map to display

    How do I make stereo figures?

    You need to save both views and assemble a composite figure using illustrator, powerpoint, or photoshop. Set up your view and ray trace and save two files using these commands. (1200,1200 is the size of the image in pixels - use whatever you need)

    ray 1200,1200, angle=3

    png view1.png

    ray 1200,1200,angle=-3

    png view2.png

    Using an external program, assemble the figure. The separation between images should be 6 cm (or close to it). If you used pymol to generate the figures, place the figure rotated by +3 degrees on the left for wall eye stereo. Check correctness by using a stereo viewer (we have one in Room 526). For cross-eye stereo, the figure rotated by -3 degrees will be on the left. (If you find these instructions to be backward, please tell me.)

    OK, I've got the figure. How do I label it?

    In Illustrator or Photoshop, show rulers and/or grid lines. Add labels to both sides such that (a) the vertical coordinate is identical and (b) the horizontal distance to the feature of interest is the same. This will cause the labels to float near the feature.

    Movies anyone?

    In this example, the protein is rotated through a full 360 sweep about the Y-axis over 120 frames

    load test/dat/pept.pdb # load a structure

    mset 1 x120 # define the movie

    util.mroll(1,120,1) # issues mdo commands to create full rotation over 120 frames

    Don't forget to save the movie.

    How do I run a script?

    Save the script on your computer. Choose File -> Run and choose the script your wish to run. You can create your own scripts too. If you create a script and think it may be helpful to others, please send it to me and I'll make it available to everyone.

    How can I display electrostatic maps in pymol.

    APBS does grasp-style electrostatic calcuations and is a pymol plugin. It's installed into pymol on django. The pymol apbs plugin does not seem to recognize metal ions. Delphi is available on django for electrostatic calculations.

    I want to draw a packing diagram

    Generate the symmetry related molecules using coot (show symmetry, save symmetry molecule and click on one you wish to show in the figure.) After saving pdb files for all of the molecules in the unit cell, start pymol and read in all the pdb files. In the scripting window, type show cell. Voila! There it is.

    How can I color by B in grayscale

    Install the color_b plug in from the scripts page (link on software page). Follow the instructions