Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    Alexander Rose
    @arose
    @tonyyzy, yes just add a contact representation, this will display non-covalent interactions.
    Tony Yang
    @tonyyzy
    Ty!
    Tony Yang
    @tonyyzy
    A followup question, is there a convenient way of recreating the PDB ligand view king of graph? or I have to filter out the non-interacting residues in ngl
    DAlvGar
    @DAlvGar
    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 :)
    Alexander Rose
    @arose
    No, there has been no work in NGL. When support for measurements will be added to molstar.org this feature will be supported. Notably it is possible in Mol* to create structures from multiple models/files transparently.
    Peter Schmidtke
    @pschmidtke
    Is it then reasonable to say that for future integrations and developments we should rather follow Mol* than NGL?
    Alexander Rose
    @arose
    Hi @pschmidtke, yes, that is the way forward. Feel free to write me an email if you want to know more where we are headed and how you could contribute and steer.
    Tony Yang
    @tonyyzy
    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/
    Alexander Rose
    @arose
    The issue you are describing usually arises from the multisample antialiasing (MSAA). Make sure you are using the latest NGL version. If the problem persist try to set the 'sampleLevel' parameter of the Stage object to 0. This will switch of the MSAA.
    Tony Yang
    @tonyyzy
    Can confirm using dev35. I will give MSAA a try tomorrow, thanks alot!
    Peter Schmidtke
    @pschmidtke
    image.png
    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
    Fred Ludlow
    @fredludlow
    Is that a specific example or one you've created? And it what way does the surface look different?
    Peter Schmidtke
    @pschmidtke
    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)
    Fred Ludlow
    @fredludlow
    Ah, I see, that's rather hidden in the documentation: You want radiusType: 'vdw' (the default is 'size', which hopefully explains the difference you're seeing)
    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
    Tony Yang
    @tonyyzy
    Hey people! I know mdsrv is not under active development any more but is there still place to get help?
    Johanna K. S. Tiemann
    @j0kaso
    Hey Tony! Sure! Best would be an issue or ask directly ;-) btw, I'm currently working (slowly) on a new release, just busy as usual...
    Tony Yang
    @tonyyzy
    @j0kaso Hey Johanna! That's awesome! Let me know if there's anything I can help with the dev process, I have some experience in python/js/web and I do hope to set up mdsrv to better share my MD data.
    Currently having a bit trouble setting up mdsrv under macos with apache, will ask when I have a more specific problem.
    Tony Yang
    @tonyyzy
    Interestingly I just had a meeting on data management and I think in the field of MD, we are doing a bit poorly on FAIR data sharing principle. AFAIK, there's no central repository for MD data? Maybe we can build a framework around mdsrv to facilitate the sharing of trajectories.
    Johanna K. S. Tiemann
    @j0kaso
    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 ;-)
    Tony Yang
    @tonyyzy
    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
    Marcin Wojdyr
    @wojdyr
    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/
    Alexander Rose
    @arose
    That is great news @wojdyr, wonderful work! This seems very new but will you make the mtz/ftt handling lib available as a package? Happy to help.
    Marcin Wojdyr
    @wojdyr
    @arose I'll do it at some point, when I have a better grasp of wasm and Emscripten. If you'd need it sooner rather than later let me know.
    Alexander Rose
    @arose
    Ok, will do, thanks
    Marcin Wojdyr
    @wojdyr
    I'll upload everything to npm later on
    LunarLanding
    @LunarLanding
    Hey, how would I make the nglviewer autoplay?
    DAlvGar
    @DAlvGar
    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.
    sneshyba
    @sneshyba
    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!
    GaryO
    @garyo
    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
    Peter Schmidtke
    @pschmidtke
    Hi. Is it possible in NGL to view symmetry mates of a crystal structure? I saw some symmetry operations in the source code but couldn't find any sample code showing that sort of functionality.
    Fred Ludlow
    @fredludlow
    You can set the assembly parameter on a StructureComponent. You can try it in the webapp, load a structure (e.g. http://nglviewer.org/ngl/?script=color/atomindex), open the menu for the structure and select Assembly 'UNITCELL' or 'SUPERCELL'
    Peter Schmidtke
    @pschmidtke
    Thanks for that @fredludlow !
    DAlvGar
    @DAlvGar
    Hi guys! I am trying to correctly display the bond orders for ligands inside a PDB structure. I have an external SDF from which I could read the bond orders. So I have a couple of questions:
    1) Can I alter the bond order in the displayed structure without modifying the PDB file?
    2) Any tip on how to match atoms/bonds between the SDF and the PDB? :)
    any help is very welcome!
    Fred Ludlow
    @fredludlow
    Is it from the public PDB, or just a file in PDB format? If the former then MMTF format already has bond orders.
    If you can rely on the atom order being correct or some other foolproof atom mapping then you can update the bond orders directly in NGL (using the internal structure.getAtomProxy() and related methods)
    If you can't rely on the atom order, I'd probably use a toolkit (rdkit or openbabel) to generate the mapping from one . There's a good writeup here: http://practicalcheminformatics.blogspot.com/2018/09/assigning-bond-orders-to-pdb-ligands.html
    Then with the mapping you can save in the "not standard but everyone uses it" PDB multiple-bond format (which NGL supports): Basically, CONECT records are repeated:
    CONECT 1 2 2
    would mean a double bond between atoms 1 and 2
    (The key part of the recipe, in RDkit, is AllChem.AssignBondOrdersFromTemplate)
    Peter Schmidtke
    @pschmidtke
    Hi, what happened to the api documentation of NGL, is it still available somewhere?
    DAlvGar
    @DAlvGar
    Thank you @fredludlow we finally went for the option you recommended to display bond orders by modify the CONNECT records and it works perfectly fine. You're the best! :)
    Peter Schmidtke
    @pschmidtke
    thanks ... that was gone for a while, no? :)
    GaryO
    @garyo
    Could have been, I don't know.
    Dominik Gront
    @dgront
    Hi! Is it possible to change coordinates of a structure already displayed by NGL so the graphics will change accordingly? E.g. to move an atom...