Subject: Announce: ZoomSeq -- sequence browser for VMD

From: Barry Isralewitz <[email-masked]>
Date: Thu, 28 Dec 2000 15:52:58 -0600

Hello,

	Announcing ZoomSeq 0.9a, a sequence browser for VMD.

	ZoomSeq is a TCL script, for the free molecular graphics
program VMD, that provides a zoomable sequence browser for protein
molecules.  Residues are selected in the sequence window, and will
appear highlighted in the molecular structure in the VMD's OpenGL
window.  Conversely, label a residue in the OpenGL window, and the
selection appears highlighted in the ZoomSeq window.

	In its current state, I've found ZoomSeq especially helpful
for keeping track of position in a large protein, and for highlighting
large sections of a molecule all at once, while still having a "global
view".  I'm working on adding options to display additional columns in
ZoomSeq, using various remote servers to add profiling methods
(e.g. hydrophobicity) and database lookups (e.g. similarity scoring).

	You can access ZoomSeq at:

http://www.ks.uiuc.edu/Research/vmd/script_library/categories/sequence.html

	The README file is inserted below.	

	Note that pre-1.5 versions of VMD won't work with ZoomSeq, you can
download the latest version of VMD (for free) at:

http://www.ks.uiuc.edu/Research/vmd/	

	Of course, please let me know about any bugs, suggestions,
questions, or interface concerns.
			
					Cheers,
	
					Barry 

  The ZoomSeq README
=====
ZoomSeq 0.9a -- a sequence browser for VMD

Barry Isralewitz <[email-masked]>   Dec 28, 2000

---

ZoomSeq is a TCL script for VMD that provides a zoomable sequence
browser for protein molecules.  Residues are selected in the sequence
window, and will appear highlighted in the molecular structure in the
VMD's OpenGL window.  Conversely, label a residue in the OpenGL
window, and the selection appears highlighted in the ZoomSeq window.

--

Running ZoomSeq
---------------
	1. Start vmd
	2. Load a molecule.  (It will be "molecule 0")
	3. type 
		source zoomseq.tcl
	    into the "vmd console" window.
	4. Wait a few seconds for setup calculation.
	5. The ZoomSeq window appears.

Display
------
	The first column displays residue number, residue name, and
chain.  The second column displays B-factor.  The third column
displays color-coded secondary structure.  (See "Coming Soon" for
upcoming data types for columns.)

	When zoomed out ( Zoom < 1.00), residue numbers may be
skipped, but the number of the last residue is always displayed.

Controls
--------

Sequence selection:
	
	Click anywhere in the ZoomSeq sequence listing to select a
single residue.
	
	For multiple selections, click and drag the 'marquee' to surround 
the residues you want to highlight.  Multiple marquee selections can be made,
they are cancelled when a single selection is made.

Sequence zoom:
	The Zoom Slider controls the vertical size of the residue
display.  The scale of '1.00' is about 8 pixels per residue.  Slide
the control with the left mouse button to see the sequence grow and
shrink, click with the center mouse button along the slider track to
jump to a zoom setting.  Zoom settings less than 1.00 are useful for
proteins of more than 150 residues.
	 The right-hand vertical scroll bar lets you scroll through
the sequence if the zoom setting makes the sequence longer than the
ZoomSeq window.

Structure selection: 

	1. Set mouse to 'Pick' mode (i.e. choose 'Pick Atoms' in VMD
Mouse menu, or press the "1" shortcut key).
	2. Click on a residue.  It will appear highlighted in yellow
in the structure and in the ZoomSeq window.

Details/Hints
-------------

	ZoomSeq highlights residues with thick yellow bonds.  If your
current rendering would obscure these, you will not see the selection.
Th defaults for all renderings (except Surf and MSMS) work fine with
ZoomSeq.

	Every residue in molecule 0 with a "CA" atom should appear in
the sequence list.  ZoomSeq will work with multiple chains correctly,
but may have problems with proteins with multiple segments.

	ZoomSeq always sets at least 1 residue highlighted. If you need
to turn the ZoomSeq selection off, just change the ZoomSeq entry in
the Graphics VMD menu from 'Bonds' to 'Off'.  The setting will be
restored with you next ZoomSeq selection.

	Since ZoomSeq displays secondary structure, there might be a
pause at startup for secondary structure calculation.

	When ZoomSeq starts, it makes a new representation in the
Graphics window, and alters that representation for any selections.
ZoomSeq will complain if this representation isn't present to alter.
If you accidentally delete ZoomSeq's representation, use 'Create New'
until ZoomSeq finds a representation to change.
	
Coming soon
----------

 	Handling multiple loaded molecules. Protein profiling and
proteomics information for columns 4, 5, 6, etc. with most information
fetched from remote bioinformatics web servers.  A version should be
sent shortly to the VMD mailing list (vmd-l).  See
http://www.ks.uiuc.edu/Research/vmd/mailing_list/ to sign up to vmd-l.

	Also, look for the latest version of ZoomSeq at
http://www.ks.uiuc.edu/Research/vmd/script_library/categories/sequence.html

=====

-- 
Barry Isralewitz     Beckman 3121    Theoretical Biophysics Group, UIUC  
Office Phone: (217) 244-1612    Home Phone: (217) 337-6364
email: [email-masked]      http://www.ks.uiuc.edu/~barryi