Hi Darrell,
Thanks for the suggestion.
To make a long story short, we're publishing a new a method to assign secondary
structure elements (SSE) solely from the C-alpha atoms (with ~95% accuracy
relative to DSSP). We've compared this to backbone reconstruction schemes and
the time to rebuild the backbone atoms is simply too time consuming (about an
order of magnitude). In fact, the BBQ method claims to be "fast" but, based on
my estimates, it's actually about twice as slow as the optimized "rebuild"
program (when optimized to only rebuild the backbone atoms using basic
geometry) from the MMTSB Tool Set by Michael Feig et al. Anyhow, my
collaborator wanted to write a PyMOL plugin which will assign the SSEs using
our program (for each state) and then display them nicely in PyMOL. This
doesn't seem to be possible in PyMOL without reconstructing the backbone atoms.
Yes, we can color each SSE accordingly but I was hoping that there was a better
solution.
Best,
Sean
> From: [email protected]
> To: [email protected]; [email protected]
> CC: [email protected]
> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
> Date: Wed, 4 Jun 2014 21:18:27 +0000
>
> Hi Sean,
>
> If you're doing this for illustrative purposes, why not just build the
> inferred backbone? You could use BBQ, among many others:
>
> http://biocomp.chem.uw.edu.pl/tools/bbq
>
> FWIW,
> Darrell
>
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
>
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
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> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
>
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>
> From: Sean Law <[email protected]<mailto:[email protected]>>
> Date: Wednesday, June 4, 2014 4:17 PM
> To: "Sampson, Jared" <[email protected]<mailto:[email protected]>>
> Cc:
> "[email protected]<mailto:[email protected]>"
> <[email protected]<mailto:[email protected]>>
> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
>
> 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: [email protected]<mailto:[email protected]>
> To: [email protected]<mailto:[email protected]>
> CC:
> [email protected]<mailto:[email protected]>
> 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
> <[email protected]<mailto:[email protected]>> 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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