Hi Sean -
I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s
part. Rather, I think it may have something to do with two facts: 1) unlike
loops, sheets represented in automatic mode are not radially symmetric; and 2)
unlike helices, the orientation of the sheet at a particular CA atom cannot be
determined by its immediate neighbors. I haven’t had a chance to look at the
relevant source, so I can’t confirm this at the moment, but it seems likely to
me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane
of a sheet, and without this information, instead of guessing at its
orientation, it omits the sheet entirely. (This also appears to be the case
for other non-radially symmetric modes, including dumbbell, rectangle, and
oval.)
Could you get by using different colors to indicate your SS assignments in
another cartoon mode?
Cheers,
Jared
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jun 4, 2014, at 1:50 PM, Sean Law
<magic...@hotmail.com<mailto:magic...@hotmail.com>> wrote:
Hi PyMOLers,
I have a c-alpha only model and I would like to visualize both helices and
sheets based on my own custom SS assignments (via "alter"). Altering a
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be
visualized. However, altering a residue's SS assignment to sheet (ss="S")
causes that residue to disappear. Again, this is c-alpha only and I am
visualizing in "cartoon automatic" mode.
Any suggestions for visualizing the sheets in this case would be greatly
appreciated.
Best,
Sean
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