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
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
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 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 f
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 she
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 par
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
Hi Folmer,
> I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04
> (reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line
> after startup).
looks like you should do a clean rebuild (remove the "build" directory).
> When the bg_color is set to white (also
Hi Thomas,
2014-06-04 18:02 GMT+02:00 Thomas Holder :
> Hi Folmer,
>
> > I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04
> (reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line
> after startup).
>
> looks like you should do a clean rebuild (remove th
Hi all,
I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04
(reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line
after startup).
When the bg_color is set to white (also gray, it seems) the text in the
main window of PyMOL is missing (revealed when pressin
