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

1 Comment »

  1. Because of the very nature of bicycling, riders are left at a distinct disadvantage.
    Throughout the study of Engineering Mechanics the principles
    of three Newton’s Laws of Motion are used invariably.
    For this reason, all cyclists bike enthusiasts
    should know their rights if injured on a bicycle at no fault of their

    Comment by bicycle — September 14, 2015 @ 8:25 pm | Reply

RSS feed for comments on this post. TrackBack URI

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

The Rubric Theme. Create a free website or blog at


Get every new post delivered to your Inbox.

Join 31 other followers

%d bloggers like this: