How To Draw Protein Topology Diagram

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TopDraw - Version: Sep 2002

TopDraw is a sketchpad for drawing topology cartoons of proteins written in Tcl/Tk (Tcl/Tk is installed by default with near unix variants and is available for most if non all platforms). Information technology does not calculate topology from a PDB file, but simply allows you lot to sketch a topology derived from some other source (my favourite is HERA - if y'all run PROMOTIF on your poly peptide, you get a .her file which is a postscript file containing the HERA topology.
(c) 2000, 2001 Charlie Bail  Charles.Bond@uwa.edu.au

New Reference: Bond,C.S. (2003) Bioinformatics 19, 311-2.

• Easy sketching of poly peptide topologies
• Relieve/Open up function for reusing/editing previous drawings
  
• Postscript output for printing/publication
• Runs (probably)  on all common platforms (anywhere Tcl/Tkv8 will run).
• Horizontal or vertical helices and strands
  
• New version allows diagonal connections

Screen Shot (click for larger version):

I wrote information technology because there was a lack of such software - I spent hours creating a topology diagram with a drawing program for a publication and got iv or 5 emails subsequently request which software I used. While Tops/XTopsprovides a route to automated cartoon generation from a PDB file, the cartoon fashion of XTops is not a style I like.

If you take any good ideas for improvements, or spot any bugs, allow me know and I will try to implement/set up them. If you have whatsoever customisations which could be included, permit me know. I am not a developer and this lawmaking is certainly not bug proof. It is provided in skillful faith but with no warranties whatsoever. If, for whatsoever reason, y'all feel that you lot cannot have responsibility for any impairment the use of this lawmaking might cause to your hardware, software, data or sanity, then do not install it. Come across the meridian of topdraw for GNU General Public License terms. Unix: To use topdraw,  download it, make it executable and put information technology in your path. You lot may need to edit the beginning line to reverberate the location of tcl on your system. You may even need to install Tcl/Tk v8 or higher. On SGIs, Tcl/Tk from http://freeware.sgi.com is suitable.
Windows: Install Tcl/Tk v8 or higher.   Download TopDraw and relieve it equally TopDraw.tcl
Unix: From the control-line type topdraw
Windows: Click on the TopDraw.tcl icon

Select an particular type by clicking on information technology. (Colours are determined by the choice boxes, not the color on the icon!)

Select fillcolour, linecolour and linewidth, and then place the particular on the sheet by clicking at the correct position.

Move it by dragging it with middle mouse button.

Delete information technology past clicking 'Delete' then clicking the unwanted detail.

To place text, set the fontsize and colour and blazon the text in the box, followed by Enter/Return. Then you can place/motion/delete it as described above.

If you are going to scale the last epitome to a new size for publication, make sure that you apply a large-enough font size. A final size of 8pt is the smallest commonly accustomed, and then if you lot will need to scale the figure down by a cistron of 2, then select font size 16.

HINT: If in desperation you accept finished a circuitous drawing and subsequently want to change the font size or some colours, this tin be achieved by editing the saved file in a text editor and then re-reading it into TopDraw. You lot will see lines similar this:
helixtop Dark-green 375 500 3 DarkGreen
line01 Green 375 550 iii DarkGreen
text Blue 275 417 18 Helvetica-Bold D
For text objects, the fields are "Object_type fill_colour x-coord y-coord font_size font text".
For other objects, the fields are "Object_type fill_colour x-coord y-coord line_width line_colour".

Objects can't be pushed underneath previously drawn objects. Place background objects outset.

If you lot wish to motility everything (e.one thousand. you started besides close to the edge), activate the \"Move all objects\" button.

Go along your drawing to the lower left side of the canvas to make further processing of postscript files easier.

The PostScript output is written using a native Tcl/Tk command. This is fully befitting PS. It should be readable by any postscript viewer (ghostscript, ghostview, ImageMagick, gimp are all freely available). If your sketch is on the far right of the canvas, it may appear 'off the page' with some viewers.

To gear up a figure for publication, I salve as Postscript (east.g. test.ps), run ps2epsi from the ghostscript package ('ps2epsi test.ps') to produce encapsulated postscript (test.epsi) which is accepted past most publishers. EPS files tin can be scaled to any size with no loss of resolution. Alternatively, this tin can be converted to whatever other epitome type with ImageMagick ('convert exam.epsi examination.tif'). Tcl/Tk for Windows (I have V8.iii) seems to leave some ovals opaque. This only affects the cursor, non the finished image, then I shall wait for TK to be fixed rather than work around it.

Source: https://bondxray.org/software/topdraw/topdraw.html

Posted by: johnsonbefteeprishe.blogspot.com

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