CONTENTS

1. What is VHMPT

2. How to install it

3. How to use it

4. Some notes

1. What is VHMPT
VHMPT is a graphical Viewer and editor for Helical Membrane Protein Topologies. It is a program that can automatically generate a schematic 2D topology for a protein with transmembrane helices; the input requires only the protein's amino acid sequence and sequence range of its helices. Through an interactive graphical interface, VHMPT allows users to modify layout of the generated topology, as well as annotate with arrows and texts. In addition, with a multiple-sequence alignment, VHMPT can color-code the degree of conservation for each of the aligned amino acids, thus highly conserved (or variable) amino acids or topology regions of the interested protein can be readily recognized and visualized in contrasting colors.

2. How to install it

VHMPT was written in Tcl/Tk. Therefore, before installing VHMPT you need to install Tcl/Tk (version 8.0) first, which you can download from
 

for Win95/98
     tcl805.exe

for Unix
     tcl805.tar.gz
     tk805.tar.gz

After Tcl/Tk installation,  execute the following steps:

For UNIX platform

Step 0:

 Download VHMPT(vhmpt.tar.gz). Save it on the directory where VHMPT is going to be installed. For example, you can save it on /home/yourname/vhmpt.

Step 1:

 Go to that directory, e.g., /home/yourname/vhmpt in this example, and untar, decompress the downloaded VHMPT archive

cd /home/yourname/vhmpt
gzip -dc < VHMPT.tar.gz | tar xf -
 

Step 2:

 Execute

wish8.0 ./reconfig.tcl

to reconfigure VHMPT.
 

Step 3:

 Type

wish8.0 tcl/vhmpt.tcl

to bring VHMPT up.
 
 

Step 0:

 Download VHMPT(vhmpt.zip). Save it on the directory where VHMPT is going to be installed. For example, you can save it on c:\My Documents\VHMPT.

Step 1:

 Go to that directory, e.g., c:\My Documents\VHMPT in this example, and decompress the downloaded VHMPT archive. You can use WinZip to decompress the downloaded archive.

Step 2:

 Double click on the reconfig.tcl file to reconfigure VHMPT.

Step 3:

 Change directory to, say, c:\My Documents\VHMPT\tcl in this example, and double click on vhmpt.tcl.

3. How to use it

from a single amino acid sequence file

from an aligned multiple seguence file

from a conservation score file

---

reconfigure helix layout

reconfigure loop layout

label/unlabel amino acid

edit/modify annotations

other viewing functions

generate helix wheel and hydrophobicity parameters

save the edited results

appendix (.helixseq, .aa, .msf, and .score file descriptions)

4. Some notes
 

Our experience with the Tcl/Tk 8.1a2 interpreter on the Win95 platform indicated that it cannot display the control points of VHMPT. It could be that this version of Tcl/Tk interpreter is not as stable as Tcl/Tk 8.0 (patch 2). For best visualization result of VHMPT we suggest use of 1024x768 (or higher) display mode.

 

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