![]() ![]() To get a list of residue numbers in the protein and store it in a variable called sel_resid: set sel_resid get resid] set foobar measure minmax $foobar measure center $foobar This can also be used to get the minima, maxima and center of the coordinates. This can also be used to select only specific chains of the molecule set chainA To store all changes, you can then writes foobar (containing all aminoacids without hydrogens and the updated beta and occupancies) into new pdb. $foobar set beta 0 $foobar set occupancy 0 Select all atoms (except hydrogens) of the structure loaded in and stores it in foobar set foobar Īfter you have selected all aminoacids, this selection can be used to do things on it.įor example to set the beta factors or occupancy of the pdb of all aminoacids to zero. ( Tools Sequence Alignment or Stramp Structural Alignment)Įxtracting the hydrogen atoms from a molecule and manipulate the pdb file This program does a Sequence Alignment using MAFFT or CLUSTALW and also a Structural Alignment using STRAMP (Structural Alignment of Multiple Proteins) Specifying the selected atoms from “All” to “resname FOO BAR”(using the three letter abbreviation)Įxtension Tk Console opens the console for scripting in VMD set selection0 # selects all atoms in the first prot set selection1 # selects all atoms in the second prot set M # aligns the two structures $sel0 move $M # move the atoms of 0 to the aligned Showing specific residues can realized using:
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