nglviewer/ngl

WebGL protein viewer

ngl's Issues

Color Spectrum BGR by b-factor

I am trying to use ngl to create a visualization for a webserver. Is there a way to color by b-factor and set the color spectrum. For example, everything below a b-factor below 0.2 is blue, .2 to .8 is green, and .8 to 1 is red?

Thanks!

Non-polymer molecule recognised as polymer in selections

For instance in PDB 4jjk, for ligand molecule FOL. If I use selection string: :A and polymer, the FOL molecule is included in the selection, when it shouldn't because it is not part of the protein chain.

User-friendly API for geometric primitives

The current methods for building geometric primitives (buffer.js) do not appear to be designed for use by end users. Adding some documentation would be a great first step, as the arguments are often hard to guess and there are many similarly-named functions (e.g. should I use a SphereBuffer, a SphereGeometryBuffer, or the nefarious SphereImposterBuffer?). It would also be nice to have some higher-level structures, such as a method for arrows.

trilinear interpolation for coloring by volume grid data

• http://paulbourke.net/miscellaneous/interpolation/
• http://www.scratchapixel.com/old/lessons/3d-advanced-lessons/interpolation/trilinear-interpolation/

Performance of NGL.ColorMakerRegistry.addSelectionScheme( selection_scheme )

Hello. I got color changing to work. I am now dealing with performance issues. There are a lot of things I can do on my end to improve performance of my webapp. However, I need some insight into the NGL.ColorMakerRegistry.addSelectionScheme( selection_scheme ) function.

I have noticed this function is O(N^2), where N is the number of selections in selection_scheme. I'm not sure why this is the case, but it may have something to do with the way jQuery works. For example, if N =130, NGL takes 968ms, but at N=2492, it takes 22571ms. My highest theoretical N so far is around 7000, although I may never see that in practice. That would take around 90,000ms to run. That's quite a bit too much for an interactive application.

Can you think of a better faster way to do this? Would combining selections be faster? For example, which is faster?

red, 10-50
red, 70-80

OR

red, 10-50 or 70-80

I know with Jmol and PyMOL, if I tried to put too many ORs together, it would crash. Please advise,

Thank you

Chad

Add post processing framework based on three.js passes

interesting post processing passes include

• cel shading/edge detection/highlight
• antialiasing (taa, msaa, smaa)
• ssao
• vignetting
• depth of field

Extend picking to measurements (distance, angle, dihedral)

The picking code is sufficient but some representations/helpers are needed to display the measurements.

Wishlist: smoothing traj

Just like vmd.

In python we can use scipy (same as mdtraj) for traj smoothing. Not sure about what u want for js side.

alpha (opacity ) value?

@arose

does ngl support alpha option?

(http://3dmol.csb.pitt.edu/ check lower section)

Better cartoon arrows

Currently cartoon arrows have no sharp transition from and to the rest of the cartoon. This is especially apparent with few segments.

To solve this, additional sets of vertices need to be added at the transition points.

Near clipping not working for line-based representations

Setting the near clipping plane does not effect line-based representations (e.g. line, trace, ...). This is due to missing shader support for custom clipping planes in the line shader.

wishlist: option for zoom, speed, ...

I am myself using VMD for visualization and there are few things I want to customize in in ngl

• camera: orthographic or perspective (I normally use orthographic camera)
• zoom and rotation speed: Most of viewing packages make me feel the molecule is very heavy when rotating. It's great if ngl allows user to config (right now I need to change js file)

wishlist: shortcut key for "Translate" (T) and "Rotate" (R)

currently ngl uses right mouse button for translating molecule. But using ring finger to push seems requiring more press. What's about adding shorcut key T (same as VMD) to switch to translate mode to be used with index finger? add adding 'R' to go back to Rotation mode.

PS: since I am using VMD and find it very convenient, I will suggest some nice features (I think).

Add support for BIRD molecules

aka PRD

Wishlist: option change movie speed

http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node3.html

Parsing of the embedded structure in Gaussian98 Cube files

The atom line parsing can be done inside the NGL.CubeParser class and similar to the NGL.GroParser._parse. The atom elements need to be assigned from the number code in the atom lines. To complete the structure, post-processing as in NGL.StructureParser is required.

Further, the NGL.Stage.loadFile method needs to be adapted to create two components for the Cube file, a SurfaceComponentand additionally a StructureComponent.

PSF file parsing

See http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html for a format description.

Only atom and bond sections.

There is an example file ala.psf in the repository.

Unloading files

I'm not sure the best way to unload a file. I only need one mmCIF file loaded at a time, at least in the near future. What code do I run as soon as I know I'm going to need a different file?

Also, when I accidentally loaded a second structure, WebGL crashed. I'm not sure if that is a bug or not. It may just be that my computer ran out of memory when trying to do that. I may experiment with loading multiple large structures another time and test the limits.

Superimpose sub-selection

It is often useful to superimpose structures based on a single chain or selection. The most natural (for me) way to do this in NGL would be to filter two structures to the desired selections, superimpose them, and then remove the filters to show the unaligned portions as well. However, the superposition gets updated automatically after changing the filter. Should this behavior be changed to only update the superposition after manually selecting the Superpose option, or is there another way to superimpose based on a selection?

Problems with API documentation

Hello. I have found at least one spot where the documentation is wrong. I'm looking at this page, http://arose.github.io/ngl/doc/#API_reference/Object/ColorMakerRegistry

You have the following example,

// color residues 1 to 100 in red, 101-200 in blue and the remaining in white
var mySelectionScheme = NGL.ColorMakerRegistry.addSelectionScheme( [
[ "red": "1-100" ],
[ "blue": "101-200" ],
[ "white": "*" ]
] );
// apply colorscheme to an existing representation
repr.setParameters( { color: mySelectionScheme } );

In order to make this work, I had to change the : to , and change color to colorScheme, like this.

// color residues 1 to 100 in red, 101-200 in blue and the remaining in white
var mySelectionScheme = NGL.ColorMakerRegistry.addSelectionScheme( [
[ "red", "1-100" ],
[ "blue", "101-200" ],
[ "white", "*" ]
] );
// apply colorscheme to an existing representation
repr.setParameters( { colorScheme: mySelectionScheme } )

What did you intend?

Chad

Support for entities from mmcif/pdb files

This includes storing the information (list of chains) and allow using it for selections.

allow different/custom radii per atom

Especially for surface calculation. Important when visualizing calculation done with different/custom atom radii, e.g. from APBS.

Add useWorker as a parameter for file loading/parsing and creating of representations

• loading/parsing
• representations

PDB format: insertion code support

The insertion code is currently not parsed.

See http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

Adding support has consequences when comparing atoms for identity where at least one has an insertion code set.

add parser for dxbin format

dxbin is the binary variant of the dx format used by apbs

• Electrostatics/apbs-pdb2pqr#216
• https://github.com/Electrostatics/apbs-pdb2pqr/blob/69faa4730c5187ff3a07d6cfd1058a1f9ae5b50e/apbs/src/mg/vgrid.c#L809

Make simulation time of a frame available

• add methods that calculate or estimate the simulation time for a given frame in
  lib/trajectory.py
  • DCD (seems not to be supported)
  • XTC/TRR
  • NetCDF (not always available)
• add frame time to the binary frame data send to the client (not that this fill break the client)
• change client to accept frame time in the binary frame data (https://github.com/arose/ngl/blob/dev/js/ngl/trajectory.js#L535-L536)
• GUI element to show the frame time

make sure file downloading works on all platforms

Currently downloads are triggered by NGL.download( data, filename ).

See also: https://github.com/eligrey/FileSaver.js/

Multi-touch zoom not working on hybrid laptop

I have a Chromebook with both a touch screen and a touchpad. I can zoom using my touchpad but not using multi-touch on the touch screen.

downsampling of volume grid data

• during file parsing
• for rendering

Best guess for representation

This is my wish list but might be very low priority.

Supposed I have a molecule and load to ngl. I do not have artistic eye but wanting to have nice rendering. I just want to have an option, such as 'I am lucky' to have ngl to o make best guess to make nice representation for me. (So I can make good figure for publication)

add example of how to use the library with require.js

...

Support COMPND record (pdb) and entity category (mmcif)

This includes (1) parsing the data from the files and (2) providing a mechanism to select parts of the structure based on it.

http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/entity.html

Generally this kind of annotation should make it more easy for a user to select certain parts in big molecules/assemblies like the ribosome.

Compatible Chain IDs

Hello, great project. I have an issue though.

In mmCIF format, you are using label_asym_id for the chain names. On it's own, that seems reasonable. However, the PDB and PyMOL, and maybe others use auth_asym_id for the chain names. Do you think NGL should use auth_asym_id as well in the interest of compatibility? You know a lot more about your program and these file formats than I do. I'm sure you will come up with a reasonable solution.

no bond for modified nucleotide

Please check this

import pytraj as pt
import nglview as nv

traj = pt.load('f2.pdb')
view = nv.show_pytraj(traj)
view.representations = []
view.add_representation('licorice')
view

file: https://github.com/hainm/amber_things/blob/master/things/nucleic/f2.pdb

(modified nucleotides: AF2, GF2).

Does ngl has function to guess bond? if not, does it have option to add bond_indices (pytraj has bond info).

Wishlist: Autorotate

Good for demos would be an auto-rotate option that just continuously rotates model until mouse takes over.

Fully support chains for biological assembly generation

Currently the transformation matrices for a specific biological assembly must all be applied to the same set of chains. However in PDB entries like 4OPJ two different matrices need to be applied to two different sets of chains to create a biological assembly.

Before I start with this I will implement the use of bitsets to represent atom selections which will allow easier and more efficient combination of selections.

zoom in/out

Hi

Does ngl support zoom?

Error handling

• Worker
• Parser

Allow drawing of cylinders between separate structures

• could be a representation that is linked to multiple structures
• one question is if atom selections are useful as they do not support selecting a specific structure (which could be another feature request)
• an implementation might be similar to the DistanceRepresentation with the atomPairparameter

Support for loading parameter in mmtf parser

to bring it in par with all the other parsers

• asTrajectory
• cAlphaOnly
• firstModelOnly

Async parsing of Gaussian98 Cube file

This can be done by processing the file lines as chunks with NGL.processArray as in NGL.GroParser._parse.

defective image scaling/export

for image exports with scaling > 1 the resulting figure is wrongly composed (e.g. like a puzzle)

option to retrieve image from stage.exportImage

currently it always triggers a download

Error in helixorient calculation

The center point calculated by the helixorient algorithm is way of in PDB entry 4YVS for some residues.

Caching

Parsing is one of the slowest steps of this program. I use very big macromolecules, and the parsing makes my program appear unresponsive. I'd like to minimize that.

1. How do I put up some status messages on the screen?

2. Is it reasonably possible to cache parsed structures? In MATLAB, I save and load in .mat format instead of reading in the pdb every time. Could we do that here in JSON format or something? Although it would have to be gzipped too to minimize transfer time between the server and client.

I could help code this with some direction, I don't know the inner workings of this program yet.

Thanks.

Simplify initialization for builds/non-development mode

Since the normal builds contain all assets there is no need to do async initialization. This is only needed for development mode where a number of assets loaded async. Basically get rid of the callback in NGL.init( callback ). Maybe get rid of the whole function for builds.

Clean up api of the Structure and Proxy classes

Add graphical representation of the unitcell box

As a representation that can be added to a structure component.

local file system support

Standalone NGL Viewer does not always work if used from local filesystem (file:///...). The error only shows up in Chromium, in Firefox everything works fine. The problem also disappears if security policies in Chromium are relaxed deliberately with "--allow-file-access-from-files".

wishlist: camera: orthographic or perspective

option to change the camera type (and can be changed in notebook)