Hi Sean,
Maybe this is useful:
http://sourceforge.net/p/pymol/mailman/message/31618301/
Cheers,
Tsjerk
On Wed, Jun 4, 2014 at 10:17 PM, Sean Law <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
> To: magic...@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 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> 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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--
Tsjerk A. Wassenaar, Ph.D.
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