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 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 ;-), 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. 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?! 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?? 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! 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. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent with [ProtonMail](https://protonmail.com/) secure email. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
