Drawing Transmembrane regions

Lee F. FrankKolakowski lfk at receptor.mgh.harvard.edu
Fri Feb 25 10:00:17 EST 1994

On Thu, 24 Feb 1994 18:22:17 GMT,
coady at ERE.UMontreal.CA (Michael Coady) said:
> In article <1994Feb24.113629.1 at mcvax2.d48.lilly.com> books at mcvax2.d48.lilly.com writes:
>>Published articles have tramsmemebranes peptide sequences drawn to
>>illuastrate the transmembrane regions in the lipid bilayer. The
>>amino acids are enclosed in circle and the circles are connect like
>>beads on a string. Is there computer program availible to do this
>>type of drawing? How do people create this type of figure? I am
>>doing this by hand and it is not easy! Thanks DPSMITH
> Dear Dennis,
> 	This question gets asked regularly and I've never seen any responses
> posted.  Unfortunately I don't have an answer for you, but if you get any,
> then I hope you'll post them because I'd like to have a program that 
> does that too.

Unfortunately this is something that most do by hand.

I work on G-protein--coupled receptors and have made a template for a
prototypical receptor.

I have also make one with the amino acid sequences for each receptor I
work with.

I use MacDraw for this (even though I prefer Unix) because the program
is relatively simple and faster than Unix drawing programs.

I could put a binhexed version of one of these figures out for FTP.

The other thing that helps is to use the layers option.
I put the circles and the letters on one layer.
The Text on another layer.
Posttranslational modifications on another layer etc.

The biggest pain is not the placement of the beads, but the letters
within the beads. These need to centered with each bead. So that is at
least 300 centering operations.

How could this be automated?

One idea is to use a drawing program with a script function and a
spline routines.

Operation 1 would be assignment of the path. Ideally this would be an
editable spline.

Operation 2 would be tell the prgram how many symbols and what type
(circle, box, etc) are needed.

The program could then calculate how many circles of what size would
give say a 300 amino acid protein along the spline drawn.

The it would ask for the amino acid sequence and fill in the letters.

All of this would have to be on top of a regular drawing program.

This sounds a little more than a weekend hacking job.

Frank Kolakowski

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