vmd依据B-factor进行可视化

2020-02-23

pdbbfactor.tcl使用

要在VMD中可视化，请在VMD Tcl命令行上使用以下pdbbfactor Tcl脚本：

1 2	source pdbbfactor.tcl pdbbfactor adk_distance_bfac.pdb

pdbbfactor最初由Justin Gullingsrud（2004）编写，pdbbfactor.tcl脚本详情如下:

# load multi-frame pdb file, storing B factors from each frame in user.
# usage: pdbbfactor <filename>
#
# Justin Gullingsrud
# 3 September 2004

proc pdbbfactor { fname } {
  mol new $fname waitfor all
  set all [atomselect top all]
  set frame 0
  set in [open $fname r]
  set beta {}
  while { [gets $in line] != -1 } {
    switch -- [string range $line 0 3] {
      END {
        $all frame $frame
        $all set user $beta
        set beta {}
        incr frame
      }
      ATOM -
      HETA {
        lappend beta [string range $line 61 66]
      }
    }
  }
}

本教程进行了一些修改：

# load multi-frame pdb file, storing B factors from each frame in user.
# usage: pdbbfactor <filename>
# url: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pdbbfactor/
#
# Justin Gullingsrud
# 3 September 2004
#
# Oliver Beckstein, 2014-10-30
# updated for use with standard multipdb files which use ENDMDL as separators
# (END --> ENDM)

proc pdbbfactor { fname } {
  mol new $fname waitfor all
  set all [atomselect top all]
  set frame 0
  set in [open $fname r]
  set beta {}
  while { [gets $in line] != -1 } {
    switch -- [string range $line 0 3] {
      ENDM {
        $all frame $frame
        $all set user $beta
        set beta {}
        incr frame
      }
      ATOM -
      HETA {
        lappend beta [string range $line 61 66]
      }
    }
  }
}

参考文献

Example: Saving dynamic per-atom properties in B-factor