On 27/03/2022 00:17, Jon Cooper wrote:
Hello, I have been trying to put together a thing for viewing small
blocks of CCP4 electron density maps with a mobile web browser. If
anyone is interested, the current state of it is here:
http://ic50.org/jbctest14.html
Have you seen/heard about uglymol? The name is an insult but the project
is interesting.
https://github.com/uglymol/uglymol
Sorry, the link is not https yet, but nothing gets uploaded to the
server! It seems to work OK on Android and iPhone and the maps (note:
only maps; it doesn't do MTZ's, sorry) look similar when viewed in
Coot (taken as the gold standard ;-),
For the record, I've never much liked the contouring of Coot - too many
close lines and tiny triangles. I've wanted to change it for a long
time, but it's never been the most important thing to fix.
but I have a few questions about the contouring algorithm that I have
used. It is "surfacenets.js" from here:
https://github.com/mikolalysenko/isosurface
and a paper describing it is here:
https://www.merl.com/publications/docs/TR99-24.pdf
Unfortunately, my maths is not good enough to tell if it matters if
you give it fractional coordinates, rather than orthogonal. I simply
give it the electron density values on the CCP4 map grid coordinates,
which will be on non-orthogonal axes for unit cells with non-90 degree
angles. It seems to give qualitatively similar results to Coot in
these cases, so I am cautiously optimistic, but not sure.
uglymol makes the transformation that you need - so does CootVR for that
matter
https://github.com/hamishtodd1/hamishtodd1.github.io/tree/master/cvr
Here's Chris Hassall playing with it:
https://www.youtube.com/watch?v=-wfopgdN8o4
Just to be clear, this is running inside Firefox.
(It looks like he discovered a contouring bug when he zooms out)
Another thing is that the results of the contouring are sent out in
groups of 3 points which are the vertices of triangles forming the
surface. Hence, I orthogonalize them and get three.js to draw them as
just that - triangles. My worry is that, since the triangles all have
edges in common, nearly all of the contour lines (except the ones at
the edges of the map box) get drawn twice, or at least are sent to
three.js twicefor drawing, which doesn't seem terribly efficient?!
Coot used to remove double drawing. The large speed up in contouring in
the 0.9 series is a result of removing that test and just drawing the
lines twice.
Is there a nicer way of doing this? I think it might be better to have
FRODO-style contouring just on the 2D sections of the map, rather than
having lots of diagonal lines?
I think so too, especially as a larger Shannon sampling factor is now
not much of an issue.
Anyway, my 5 YO phone takes about 3 seconds to step from one residue
to the next, so it seems not too bad, although not ideal!
FWIW, Kevin Cowtan recently advertised a position to "develop next
generation web based molecular graphics software" - sounds related.
Finally, its been asked before, but is there a nice way in CCP4i2 to
output maps that cover the coordinates of the structure, rather than
the asymmetric unit? Saving maps in Coot gives the asymmetric unit,
too, although using Export Map Fragment seems the best option. I know
about doing this in the old gui with mapmask, or using phenix, so just
wondering if I've missed a way of doing this in i2, etc? I know that
suitably extended CCP4 maps are available from the PDBe EBI.
I just use a script that runs mapmask - using a GUI seems like an overhead.
Paul.
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