My software notes

March 17, 2007

align structures by PyMOL

Filed under: pymol/ molmol — kpwu @ 11:30 am

PyMOL provides a command called align to align a specific region of structures. The protein structures do not need to have to identical sequence. It’s more flexible than MOLMOL 2k.2.
The command manual copied from PyMOL is pasted here:

DESCRIPTION   "align" performs a sequence alignment followed by a structural

   alignment, and then carrys out zero or more cycles of refinement

   in order to reject structural outliers found during the fit.


align (source), (target) [,cutoff [,cycles [,gap [,extend

         [,skip [,object [,matrix [, quiet ]]]]]]]]


cmd.align( string source, string target, float cutoff=2.0,

              int cycles=2, float gap=-10.0, float extend=-0.5,

              float extend=-0.5,int skip=0, string object=None,

              string matrix="BLOSUM62",int quiet=1 )


If object is not None, then align will create an object which

   indicates which atoms were paired between the two structures


align  prot1////CA, prot2, object=alignment


fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit

Another external fitting/alignment command is called cealign, you could find a complete description at here ( .

Here are two snapshots before and after I align 1DYR to other 8 DHFR proteins. This time, all proteins have identical sequence; therefore, I use “align 1DYR, 1DAJ” to align 1DYR onto 1DAJ (all atoms to all atoms). The Tcl/Tk GUI window returned a RMS value and several detailed information.

before alignment

after alignment



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  2. […] align structures by PyMOL | My software notes – Mar 17, 2007  · PyMOL provides a command called align to align a specific region of structures. The protein structures do not need to have … align structures by PyMOL […]

    Pingback by How To Align Two Protein In Pymol | Gohowto — November 9, 2016 @ 9:44 pm | Reply

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