For info, this website of mine ('mini map aide'):
[minimapai.de](http://minimapai.de/)
should now work with MTZ files.
Thank you to Marcin Wojdyr (CCP4/Global Phasing) for letting me use gemmi
sf2map on the server to do the conversion from MTZ to CCP4 map format. I gather
it uses pocket FFT!
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent with [ProtonMail](https://protonmail.com/) secure email.
------- Original Message -------
On Saturday, May 21st, 2022 at 00:20, Jon Cooper
<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 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 <
> 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> 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.
>>>>
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