VMD-L Mailing List
From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Thu Dec 28 2000 - 14:54:20 CST
- Next message: John Stone: "Announce: Structural Biology Software Database"
- Previous message: John Stone: "Announce: VMD 1.6 Released"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hello,
Announcing ZoomSeq 0.9a, a sequence browser for VMD.
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.
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
Pre-1.5 versions of VMD won't work with ZoomSeq, you can
download the latest version of VMD at:
http://www.ks.uiuc.edu/Research/vmd/
Also, I've attached the script 'zoomseq.txt' to this email;
rename to zoomseq.tcl after saving, then follow the README instructions,
inserted below.
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 <barryi_at_ks.uiuc.edu> 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/ ===== -- Barry Isralewitz Beckman 3121 Theoretical Biophysics Group, UIUC Office Phone: (217) 244-1612 Home Phone: (217) 337-6364 email: barryi_at_ks.uiuc.edu http://www.ks.uiuc.edu/~barryi
- text/plain attachment: zoomseq.txt
- Next message: John Stone: "Announce: Structural Biology Software Database"
- Previous message: John Stone: "Announce: VMD 1.6 Released"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]