Protein Structure Distance Plots?
abonvin at volta.csb.yale.edu
Mon May 15 14:34:42 EST 1995
In article <95May14.162151edt.6166 at neat.cs.toronto.edu>
steeg at cs.toronto.edu ("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 laplace.csb.yale.edu |
| 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 file.name. 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
file.name or read from disk by the command read cluster data
file.name. The display of the RMSD natrix is done by the command
(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
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 nic.funet.fi
(2) Use the user id "anonymous" and for the password use your
user id and address (like myuserid at from.my.place).
(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 agreement.ps
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 nic.funet.fi for a limited timed.
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 csc.fi
New opinions are always suspected, and
usually opposed, without any other
reason but because they are not already
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