My software notes

March 19, 2007

sausage view of a NMR ensemble structure

Filed under: pymol/ molmol — kpwu @ 1:50 pm

Usually, a NMR structure represents the dynamics of a protein in solution. The NMR structure deposited in Protein Data Bank always contains 10 to 20 structures (states). It’s nice to generate a “tube (sausage) ” like structure to show how flexible each residue is.

MOLMOL is the best molecular viewer having this kind of function. Just load a NMR structure and run the standard macro called sausage.mac to make a sausage-view. Here is an example of 1PIT.pdb

molmol-sausage

PyMOL, however, doesn’t have built-in script to generate a sausage-view-structure. Cameron Mura in UCSD provides a nice pymol script to make this purpose. Just go to his pymol homepage (http://mccammon.ucsd.edu/~cmura/PyMOL/), download average3d.py and follow the instruction to generate a sausage-view-structure. Here is the result I made (also, 1PIT.pdb)

pymol, sausage view

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6 Comments »

  1. Doesn’t the PyMOL preset “b factor putty” (under (A)ction menu for a PyMOL object: A–>preset–>b factor putty) fit the bill? For RMSDs or R2 values, one could just hack the B factor field…

    I don’t know (haven’t looked) where the preset scripts are bundled with PyMOL, but it seems to be a R. Campbell-like histogram bin-ing –> color gradient process that changes the cartoon_putty parameters. I don’t know how to do this in a residue-specific way.

    Nice site, by the way. How do I figure out who you are?

    Comment by Ryan MB Hoffman — April 6, 2007 @ 11:44 am | Reply

  2. Hello Ryan,
    You are right,pymol does have this “b factor putty” function. I never knew it before reading your comment. Thank you for the comment.
    PyMOL is so powerful and easy to use that users can implant their own python scripts to execute them. I guess the sausage hack I referred was release before v0.98 that is the first version support sausage view.

    To figure out who I am, please check the page/(who I am). I just make an update.

    kpwu

    Comment by kpwu — April 6, 2007 @ 2:42 pm | Reply

  3. Yep — I hacked the “putty”/”sausage” functionality back into the source code of the v0.97 tree (parts of my PyMOL website are rather outdated, including the average3d.py bit), and it was subsequently incorporated into the stable 0.98 release… 😉
    Cam

    Comment by Cameron Mura — July 25, 2007 @ 4:56 pm | Reply

  4. Hi,
    I would like to know how to patch with the sausage view in
    Pymol Windows version???

    Thanks

    Comment by claude — March 12, 2008 @ 4:20 am | Reply

  5. Hi Claude,

    Unfortunately, I don’t have any Windows machine in hand. I believe you just follow the instruction from the script author to execute the python script. It should work well..

    Comment by kpwu — March 12, 2008 @ 9:03 pm | Reply

  6. Your site was extremely interesting, especially since I was searching for thoughts on this subject last Thursday.

    I’m Out! 🙂

    Comment by online stock trading advice — January 10, 2010 @ 11:07 pm | Reply


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