[Chimera-users] Molecule fusing

[Brian & Lanie Grech]

Hi Elaine and Tom

Thank you for the suggestions, I haven't had a chance to try any of them. But I hope to do this in the next couple of days.

Regards
Brian
  ----- Original Message ----- 
  From: Elaine Meng 
  To: Brian & Lanie Grech 
  Cc: chimera-users at cgl.ucsf.edu 
  Sent: Saturday, October 16, 2010 2:49 AM
  Subject: Re: [Chimera-users] Molecule fusing


  Hi Brian,
  Figure 1A shows a density map that has been segmented and colored, with an octant chopped out.
  <http://www.pnas.org/content/106/26/10644.long>


  Chimera does have tools for building multimers using symmetry information, see Multiscale Models, Unit Cell, and command "sym."  However, these just generate and place the extra copies, either as low-res surfaces (Multiscale Models) or as full atomic copies (Unit Cell).  There is no "fusing" or generating a density map from the whole assembly.  Each chain is separate.
  <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
  <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html>
  <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>


  You could get a whole assembly at atomic detail and then simulate a density map from it with the "molmap" command.
  <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
  However, that would be very inefficient and might overload your system and take forever.  That is why Multiscale Models makes the copies as low-resolution surfaces by default.  You might want to take a look at Multiscale Models and see if what it does meets your needs before trying that more drastic approach.  An easy way to try it is to use File... Fetch by ID and get something from viperdb, which will automatically use Multiscale Models to build the capsid.  Besides the example given in the dialog, I like 1pov (poliovirus) and 1bbt (foot and mouth disease virus).


  I hope this helps,
  Elaine
  -----
  Elaine C. Meng, Ph.D.                       
  UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
  Department of Pharmaceutical Chemistry
  University of California, San Francisco


  On Oct 14, 2010, at 7:50 PM, Brian & Lanie Grech wrote:


    Hi Sir/Madam
     I want to create models which consist of multiple protein molecules, in which the individual protein molecules are fused together to form a single structure. Something like the scanning 3D maps produced by electron microscopes. Is it possible to do this with the Muliscale Models tool or some other tool or method in Chimera?

    An example of what I want to do appears in the cutaway rotavirus illustration (Fig. 1A) in Chen and colleagues paper, titled, “Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM” (PNAS, vol. 106. no. 26, p. 10644). In this illustration the yellow triangular shaped structure are multiple VP7 molecules fused together.

    Regards
    Brian Grech





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