For info, barring disasters, the mini map viewer I put together (minimapai.de) should now work with maps produced by Gemmi sf2map.
I did not realise the default axis order (i.e. fast, medium, slow) had changed. Anyway, I think it now works with both the new- and old-style maps. Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 7 Apr 2022, 01:03, Jon Cooper wrote: > 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 ######################################################################## 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/
