Hi Sean - 

I can confirm this behavior, but Iím not sure itís unintentional on PyMOLís 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 havenít had a chance to look at the relevant source, so I canít confirm this at the moment, but it seems likely to me that PyMOL uses the other (non-CA) backbone atoms to define the ďflatĒ 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 <magicmen@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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