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
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'
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? :)
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!
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
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
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)
poking around in the source i found a line called "stage.viewer.requestRender(); "...looks like that may work too!
Hi all, long time no see / write :)
Has anyone @fredludlow for instance integrated something in the NGL codebase to correctly parse MMCIF bond orders for HETATM's not from the external components cif, but from a loop section like this as supported by the standard itself:
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
5CV C32 N29 SING N N 1
5CV C32 C33 SING N N 2
5CV C38 C33 DOUB Y N 3
...
Hi everyone, we added ngl to the foldseek webserver (https://search.foldseek.com). We had the issue that we store only the C alpha trace, so we used pulchra, an existing C tool compiled to WASM, to complete the structure and show it in NGL. The code for pulchra is here: https://github.com/milot-mirdita/pulchra-wasm. I am not sure if this is useful for NGL as wasm can be quite finicky and pulchra uses some large data structures
Whats the easiest way to superpose all models within one structure?
I was hoping I could do something like this:
var s = r.structure
NGL.superpose(s, s, true, "/4", "/0")
NGL.superpose(s, s, true, "/3", "/0")
NGL.superpose(s, s, true, "/2", "/0")
NGL.superpose(s, s, true, "/1", "/0")
r.updateRepresentations({ position: true })
r.autoView()But that doesn't work.
Found a solution:
var s = r.structure
var base = s.getView(new NGL.Selection("/0 and .CA"))
for (var i = 1; i <= r.structure.modelStore.count; i++) {
var view = s.getView(new NGL.Selection(`/${i-1} and .CA`))
var superposition = new NGL.Superposition(view, base)
superposition.transform(view);
}
r.autoView()