For now, we are using different colors to indicate the SS assignments but it's not pretty. We would prefer to show the SS for both sheets and helices.

Can you elaborate on what you mean by "radially symmetric". Are there other cartoon modes where I would be able to get both helices and sheets after altering the residue's SS assignment by hand? I see what you mean by not being able to define the flat plane though.



From: Jared.Sampson@nyumc.org
To: magicmen@hotmail.com
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
Date: Wed, 4 Jun 2014 20:03:54 +0000

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?


Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center

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.


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