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Drawing Transmembrane regions

croth at pasteur.fr croth at pasteur.fr
Sun Mar 6 13:34:50 EST 1994

lfk at receptor.mgh.harvard.edu (Lee F. (Frank) Kolakowski) writes:

>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

>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 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

A less complete but easier solution might be for some nice person to
make a TrueType or Postscript font with the letters in circles. You
could then substitute the normal letters with the circled letters and
bind the text seq to curve or spline in a drawing program. 

Charles Roth (croth at pasteur.fr)

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