Hi Sean -
By “radially symmetric” I mean that a particular representation (e.g. anything
in cartoon tube or putty modes, or loops in automatic mode) is drawn as a
series of truncated cylinders or cones, so for PyMOL to draw them, basically
all it needs for each short section are two end points and a radius (or start
and end radii, in the case of the cones). If you zoom in really close, you can
actually see the boundaries between individual sections.
This differs from sheets in automatic, oval, rectangle, and dumbbell modes,
because those require extra information to define the orientation of the
“width” and “height” dimensions of the section with respect to the “length”
axis (the one along the trace of the cartoon).
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jun 4, 2014, at 4:17 PM, Sean Law
<magic...@hotmail.com<mailto:magic...@hotmail.com>> wrote:
Jared,
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.
Best,
Sean
________________________________
From: jared.samp...@nyumc.org<mailto:jared.samp...@nyumc.org>
To: magic...@hotmail.com<mailto:magic...@hotmail.com>
CC: pymol-users@lists.sourceforge.net<mailto: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 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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