Thank you to those who replied a week or two ago about this. In the end, I put a revised version here:
http://minimapai.de/ I'm not sure if that (econo) domain name is a play on words or an aide memoire ;-? Anyway, with practice, it seems to keep working for ~100 or more residues,at a time, which might even be useful to somebody ;-? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent with [ProtonMail](https://protonmail.com/) secure email. ------- Original Message ------- On Monday, March 28th, 2022 at 16:33, Jared Sampson <jared.samp...@columbia.edu> wrote: > 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 ######################################################################## 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/
