the radiusDict could probably refactored to be just a list
@pschmidtke Can mtz files provide volume data directly? I thought mtz files store reflections then you fft to create a ccp4/map/mrc file with the volume data. The ccp4/mrc format is already supported: e.g. the mrc and ccp4 examples in the gallery: http://nglviewer.org/ngl/gallery/index.html.
Hi Fred, no they don't and yes you have to go through fft indeed. I'm already aware of ccp4/mrc, map, cns and xplor format support of NGL. Just that mtz is gaining popularity and it would be interesting to get a direct support. Not sure if it's even possible (fft in js ;))
these fft implementations are usually only 1D or 2D, I couldn't find 3D fft in JS. (3D fft is based on 1D fft, so having fast 1D fft also helps). I think there is also no readily available library for parsing the MTZ format, although it's a well documented format so it is also doable. I've been thinking about implementing what @pschmidtke asked for a while, but I don't know if I ever get to do it.
Hi all! I am plotting interactions between a ligand and a protein using the Shape component and adding dashed cylinders to it and finally adding a buffer representation. With this set up I did not find how to switch the visibility of independent cylinders (eg. i want to display only hydrophobic interactions) or I want to change the color of one cylinder when it is selected. The solution i had in place was to destroy and rebuild the whole Shape component. Is there a better way? Should i create independent shapes for each cylinder? How is that performing compared to a single shape?
for the style i am not completely destroying the shape, but to set the visibility i do not see how this could be done without a separate shape. Any help is very welcome :)
Hi everybody, I've been wondering if there has been some new development since this issue (arose/ngl#323) to better treat measurements between different structures? I am implementing a measure mode where the user picks atoms to create different types of measures dynamically and I would appreciate some way to avoid concatenation if its possible :)
Hey people, king of a long shot question. When I tried to open my viewer on my phone (android with chrome browser). The visualisation area is black when I'm not touching the screen (shows when I'm moving the molecule). This problem does not exist when I open RCSB or ngl gallery (codepen) on my phone. Anyone may have any idea why this happens?
BTW, here's the viewer I was referring to, https://tonyyzy.github.io/ETviewer/
HI all, is there some documentation available how to programmatically generate a solvent accessible surface like that with radiusType vdw radius? In all the API docs we find we cannot specify that parameter and the surface is then different to what is shown in the NGL sample web app
the screenshot above is from the NGL sample app online, when you create a SAS with vow radius of the pocket, the pocket surface nearly touches the ligand (vow radii are taken into account + radius for solvent). If we do that using the function to create a surface representation of type SAS the surface looks not the same, the radii's are smaller basically. ProbeRadius is set, but we cannot set this radius type (by vow radius programmatically)
It doesn't seem to be exposed in the normal documentation, but for reference: https://github.com/arose/ngl/blob/2d84a993/src/utils/radius-factory.ts#L11
Currently having a bit trouble setting up
mdsrv under macos with apache, will ask when I have a more specific problem.
absolutely true! one of my next goals is to connect mdsrv with data sharing resources like figshare... But a central repository like the pdb isn't easy to maintain - but have a look at e.g. plumed-nest, or purpose-specific resources (GPCRmd, NMRlipids databank, ...), something like this is more likely to help in FAIR right now than waiting for a MDpdb ;-)
Thanks for the info! Never heard of plumed before but it looks very cool, a solid step towards MD reproducibility. I just got started in MD and I always ask myself if I can sanity check my inputs ;). I agree that a centralised repo definitely needs institutional support (e.g. EBI). I was more thinking about a data-sharing framework that individual lab can deploy easily as an interim solution. You are right that a public data-sharing resource is likely to be more sustainable but they always have space limitations or needs curation effort :(
BTW
MDbox looks very promising but there's no continuation of it now https://conference.eresearch.edu.au/wp-content/uploads/2017/07/Karmen-Condic-Jurkic.pdf
Hi, a year ago @pschmidtke asked about MTZ support. I've put together a wasm module that reads MTZ (using Gemmi) and does FFT (using PocketFFT). Here is a demo: https://uglymol.github.io/view/
I'll upload everything to npm later on
Hi all! I have some issues with volume maps when they use boxSize and a transformation. Here's the issue: arose/ngl#756 Does someone know where could the problem be? I appreciate any help :) I've spent already a couple of days going through the code and testing some modifications without success.
Hi @arose, I'm trying to display hydrogen bonds between two groups (RNA and solvent), and your reply to @tonyyzy on April 15 2019 suggests that one "add a contact representation". Could you point me to an example? The groups I've defined are RNA and SOL (water), and I've tried "view.add_representation('contact',selection='RNA+SOL')", which slows down the display considerably. But I'm not sure where to go from there (or even if that's even on the right track). Thank you!
Hi folks; quick user poll. Who would be in favor of a color-managed workflow in NGL (proper linear color inside, and sRGB for display)? The visual results would look "better", but certainly somewhat different. Feel free to PM me, or comment on the NGL issue: nglviewer/ngl#775