Protein Structure Distance Plots?

Alexandre Bonvin abonvin at
Mon May 15 14:34:42 EST 1995

In article <95May14.162151edt.6166 at>  
steeg at ("Evan W. Steeg") writes:
>   Does anyone know of public-domain programs for making
> distance plots ("Ooi plots")?  That is, a graphical
> representation of an inter-atomic distance matrix?
Below an old anoucement (Dec 93) for a program what should allow to  
generate what you want. It gives a ftp site from where you can download  
the program. I have checked it and it's still there.

| Alexandre Bonvin PhD           | Phone: (203) 432-5066                 |
| Mol. Biophys. & Biochemistry   | Fax:   (203) 432-6946                 |
| Yale University                | Email: abonvin at   |
| New Haven CT 06520-8114, USA   |                                       |


     Scarecrow Computing Proudly Presents version 1.6 of the fabulous
                      graphics program SCARECROW. 

SCARECROW is a program for the display and analysis of molecular
dynamics trajectories from the programs AMBER, CHARMm, Discover, 
GROMOS, HyperChem, MUMOD, YASP. SCARECROW is NOT a public domain
program but you can use SCARECROW free of charge if you follow
the lisence agreement. See the agreement form.

SCARECROW runs only on SGI hardware (so far).

Some of the new features:

Version 1.6     This is not a major rewrite of Version 1.5 but rather 
a bug fix with some new additions and some new commands have
been added. Some old commands have gone through some changes as well.

(1)     The command set window multi and set window single have been
        added. The single window mode is equivalent to the old display
        style where the structure, linear distance plot (LDP), cluster
        plot and the Ramachandran plots where displayed in the same 
        window. Now it is also possible to display the different
        plots in separate windows. To do this the set window multi
         has to be defined.

(2)     The read command has now been changed to reflect what is read. The
        command is now read coordinates type. The command to read a PDB  
        is now read coordinates pdb It is possible to read
        HyperChem coordinate and trajectory files.

(3)     SCARECROW supports now the possibility to display or analyse only  
        part of the frames in the trajectory file. With the commands set
        trajectory limits first last step or modify trajectory limits  
        last step it is possible to define the trajectory frames to be
        included. The display or analysis will now start from frame
        'first' and end at frame 'last' including every 'step' frame.
        The default is always every frame from first to last.

(4)     The quatfit program (Copyright: Ohio Supercomputer Center, David  
        Heisterberg, 1990) to superimpose two structures is now included  
        the SCARECROW package. Use the command calculate quatfit  
        seg2:res2:atm2 to superimpose two structures. The second structure
        will now be imposed on the first structure using the atoms defined
        in the list. The number of atoms in the both lists has to be the
        same but different atoms can be used.

(5)     A primitive graphical tool has been added to do a cluster analysis  
        the frames in a trajectory file. The command calculate cluster
        seg:res:atm calculates the root mean square deviation (RMSD)  
        for the defined frames. This is done by reading frame i and j and
        using the quatfit algorithm to superimpose the structures  
        to the atoms defined in the seg:res:atm list. The calculated RMSD 
        matrix can be saved to disk by the command write cluster data or read from disk by the command read cluster data The display of the RMSD natrix is done by the command
         plot cluster.

(6)     To define a new display range for a LDP or cluster plot use the 
        commands modify ldp range f1 f2 f3 f4 f5 f6 f7 f8 f9 or modify 
        cluster range f1 f2 f3 f4 f5 f6 f7 f8 f9. The new range will be
        x > f1, f2 < x < f3, f4 < x < f5, f6 < x < f7, f8 < x <f9 and x >  

(7)     It is possible to display in real stereo using the StereoView  
        Use the command set stereo on to get into the stereo mode. To get
        off the stereo mode press the escape key.

(8)     To be able to rotate or translate a molecule or a part of a  
molecule in
        respect to the rest of the system one can define a subset of the
        system and then apply the rotation or the translation to that set. 
        Use the command define atom selection seg:res:atm to define the
        atoms and then press the keypad key 5 while you rotate or  
        the molecule with the mouse. Then only the selected part gets  

(9)     There is now a method to calculate a diffusion coefficient. It's
        possible to calculate the mean square displacement from the center
        of mass for the selected atom coordinates with the command  
        msdisplacement seg:res:atm and the "atom" mean sqare root  
        for selected atom coordinates with the command amsdisplacement 
        seg:res:atm. The commands report also a diffusion coefficient.

 Most likely there is a lot more but I have lost track of the time when a
 particular new feature was included. Discover yourself!

You can download SCARECROW from from the anonymous ftp server  
Do the following:

(1)    ftp 
(2)    Use the user id "anonymous" and for the password use your
       user id and address (like myuserid at
(3)    Change directory to /pub/sci/chem/scarecrow and you can see
       the following directory.

      *** This is SCARECROW version 1.6 distribution. ***

The files are:

-rw-------   1 laaksone csc          913 Dec 17 13:00 README.FIRST

  This file (almost).

-rw-r--r--   1 laaksone csc        49939 Dec 17 10:54

  PostScript version of the license agreement form. If you haven't
  returned me one, please do it now.

-rw-r--r--   1 laaksone csc         4972 Dec 17 10:21 agreement1.6.hqx

  Agreement form (Microsoft Word for Macintosh file) as a HQX file.

-rw-r--r--   1 laaksone csc         3584 Dec 17 10:33 agreementmw.doc

  Agreement form (Microsoft Word for Windows) as a binary file.

-rw-r--r--   1 laaksone csc      1138373 Dec 17 10:20 scarecrow1.6.hqx

  SCARECROW manual (Microsoft Word for Macintosh file) as a HQX file.

-rw-r--r--   1 laaksone csc      6275011 Dec 23 08:39 scarecrow1.6.tar.Z

  SCARECROW code and libraries.

-rw-r--r--   1 laaksone csc      1077760 Dec 17 10:22 scarecrowmw1.6.doc

  Scarecrow manual (Microsoft Word for Windows) as a binary file.

(4)   Download the files (you need) using binary mode.

Please return the user agreement form if you start using SCARECROW
so I know who are using the program.

I will only keep SCARECROW at for a limited timed.


-Leif Laaksonen

Leif Laaksonen                     |  
Center for Scientific Computing    | Phone:      358 0 4572378
P.O. Box 405                       | Telefax:    358 0 4572302 
FIN-02101 Espoo                    | Voice Mail: 358 486257407
FINLAND                            | Mail:  Leif.Laaksonen at

              New opinions are always suspected, and
              usually opposed, without any other 
              reason but because they are not already

                                   John Locke

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