Hi Phoebe - Your email got me wondering about this as well, so over the weekend I downloaded BioViewer (simple and relatively intuitive, few customizable options), and iMolview (more complex user interface, with more information—e.g. sequence, chain IDs—and more granular control of representation) on iOS. Not sure if there is an Android version for either of those but if you're working with iPads, they might be worth a closer look.
Cheers, Jared On Sun, Mar 27, 2022 at 4:00 PM Phoebe A. Rice <pr...@uchicago.edu> wrote: > Oo that looks handy! > > > > And it reminds me to ask the community: if you wanted to do outreach to > high schoolers and get them to, say, look at a DNA structure, is there a > PyMol-like program that works on tablets? I see PyMol for ipad has been > discontinued. > > > > Thanks, > > Phoebe > > > > > > *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul > Emsley <pems...@mrc-lmb.cam.ac.uk> > *Reply-To: *Paul Emsley <pems...@mrc-lmb.cam.ac.uk> > *Date: *Sunday, March 27, 2022 at 11:11 AM > *To: *"CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> > *Subject: *Re: [ccp4bb] Maps on mobile phones. > > > > > > 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 twice for 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. > > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
