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composite omit map

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  • subhendu chakraborti
    Hi everyone, This might be very obvious question but I would appreciate any suggestions. I am trying to refine a structure and there is a very important loop
    Message 1 of 3 , May 1, 2010
      Hi everyone,
      This might be very obvious question but I would appreciate any suggestions.

      I am trying to refine a structure and there is a very important loop with undefined density. There is enough density, but my Ramchandran plot is not at all satisfied and the density is more like a blob, where the residues could be fit in any number of ways.

      I was wondering if making a composite omit map would help. While making a composite omit map do I delete all the residues (that I have built) in the blob or keep the residues that I have built in? Would it help to keep the residues or delete them?

      Thanks

      Subh
    • Boaz Shaanan
      Hi, The composite omit map script guides you through the process and asks which parts of the structure you want to omit, starting with the residues you
      Message 2 of 3 , May 1, 2010
        Hi,

        The composite omit map script guides you through the process and asks which parts of the structure you want to omit, starting with the residues you explicitly want to omit and then the neighbouring  region. So you don't have to delete anything from the input pdb, if that's what you meant in your question. Depending on the state of your structure (and it seems close to being complete), I wouldn't go to a too high annealing temperature either (1000 K at most, maybe even less).

         Good luck,
         
                         Boaz

        ----- Original Message -----
        From: subhendu chakraborti <i_m_subh@...>
        Date: Saturday, May 1, 2010 16:52
        Subject: [cnsbb] composite omit map
        To: cnsbb@yahoogroups.com

        > Hi everyone,
        > This might be very obvious question but I would appreciate any
        > suggestions.
        > I am trying to refine a structure and there is a very important
        > loop with undefined density. There is enough density, but my
        > Ramchandran plot is not at all satisfied and the density is more
        > like a blob, where the residues could be fit in any number of ways.
        >
        > I was wondering if making a composite omit map would help. While
        > making a composite omit map do I delete all the residues (that I
        > have built) in the blob or keep the residues that I have built
        > in? Would it help to keep the residues or delete them?
        >
        > Thanks
        >
        > Subh
        >
        >
        >
        >
        >


        Boaz Shaanan, Ph.D.
        Dept. of Life Sciences
        Ben-Gurion University of the Negev
        Beer-Sheva 84105
        Israel
        Phone: 972-8-647-2220 ; Fax: 646-1710
        Skype: boaz.shaanan‎
      • Ed Pozharski
        ... No, composite omit map will automatically exclude regions from map calculation. I may have actually confused recently the composite map and sa_omit map
        Message 3 of 3 , May 3, 2010
          On Sat, 2010-05-01 at 01:14 -0700, subhendu chakraborti wrote:
          > I was wondering if making a composite omit map would help. While
          > making a composite omit map do I delete all the residues (that I have
          > built) in the blob or keep the residues that I have built in? Would it
          > help to keep the residues or delete them?
          >

          No, composite omit map will automatically exclude regions from map
          calculation. I may have actually confused recently the composite map
          and sa_omit map (the latter will omit the residues you specify, but you
          still just have to specify them and *not* remove from pdb file).

          IMHO, however, your may get better results with solvent flattening. It
          is also possible that the loop you have is simply disordered and tracing
          it with single conformation will not work.

          HTH,

          Ed.

          --
          "I'd sacrifice myself, but I'm too good at whistling."
          Julian, King of Lemurs
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