structure display and FED

2 replies [Last post]
Julie
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Joined: 03/29/2012

The SAMPLE output (not input) command under "Structure Display and Free Energy Determination" is not functioning.
Under structure display (Kin), the following is my output and I can't figure out what each column indicates.

Thanks for helping me out

@kinemage 13367584
@text
dG = -10.70 12May11-13-47-52
@onewidth
@lmatrix 0.7071 0.7071 0.0 0.0 0.0 -1.0 -0.7071 0.7071 0.
@zclip 73.3
@vectorlist {RNA backbone UC} color = yellow
{ 5} P -333.487, -10.279, 0.025
{ 6} L -360.204, -60.666, 15.378
{ 7} L -380.520, -115.127, 25.847
{ 8} L -397.678, -171.598, 28.114
{ 14} P -404.511, -167.239, -28.157
{ 15} L -360.605, -127.797, -25.873
{ 16} L -319.861, -86.335, -15.369

Thanks again,
Julie Kim from University of Guelph

zukerm
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Joined: 11/12/2010
Thank you for writing. The

Thank you for writing. The sample output has now been restored

The ".kin" file is formatted for the KING program created for viewing molecular structures in 3D.

The format is fairly self-evident, but I am not sure about details. In the "vectorlist", the three floating point numbers are (x,y,z) co-ordinates. P means "pen down" and "L" means "line to". I created a simple and naive 3D view of an RNA structure. These structures are total nonsense. I did it for fun. They are perhaps of some value in the sense that they give the user a rough idea of what a structure might look like in 3D.

Julie
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Joined: 03/29/2012
Thank you!!!

Thanks for your reply. =)