iCn3D

Repository for iCn3D prototyping Features can be developed and tested, then submitted to the NCBI repository for long term adoption

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icn3d-protyping's Issues

png export import bug

Case 1 - works

Load a structure from local PDB file
Load state file without the "load structure" command
Save a png - note: filename is "1AZI_image_icn3d_loadable.png"
Load the saved png
Data are rendered correctly

png file

Case 2 - does not work

Load a state file with a "load structure" command
Save a png - note file name is "encoded" (1AZI-HCm6yEY61J1Wa1pN8.png)
Load the png
A server version of iCn3D is launched in new tab with a broken set of commands

png file

Executed commands:

load mmdb 1azi | parameters &shownote=1&divid=div0&mmdbid=1azi&date=20210420&v=2.24.4&command=load%20mmdb%201AZI;%20select%20main%20chains;%20color%20grey;%20select%20.A:2-17%20|%20name%20peptide%2001%20fpop%20value%20=%200.601109658;%20style%20sidec%20ball%20and%20stick;%20color%20cc0300;%20select%20.A:18-32%20|%20name%20peptide%2002%20fpop%20value%20=%200.079598829;%20style%20sidec%20nothing;%20color%20D3D3D3;%20select%20.A:33-43%20|%20name%20peptide%2003%20fpop%20value%20=%200.129321638;%20style%20sidec%20ball%20and%20stick;%20color%20cca0a0;%20select%20.A:64-79%20|%20name%20peptide%2004%20fpop%20value%20=%200.33615972;%20style%20sidec%20ball%20and%20stick;%20color%20cc5b59;%20select%20.A:80-88%20|%20name%20peptide%2005%20fpop%20value%20=%200.255505346;%20style%20sidec%20ball%20and%20stick;%20color%20cc7675;%20select%20.A:80-97%20|%20name%20peptide%2006%20fpop%20value%20=%200.335083831;%20style%20sidec%20ball%20and%20stick;%20color%20cc5c5a;%20select%20.A:81-97%20|%20name%20peptide%2007%20fpop%20value%20=%200.352149128;%20style%20sidec%20ball%20and%20stick;%20color%20cc5654;%20select%20.A:104-119%20|%20name%20peptide%2008%20fpop%20value%20=%200.327020816;%20style%20sidec%20ball%20and%20stick;%20color%20cc5e5d;%20select%20.A:120-134%20|%20name%20peptide%2009%20fpop%20value%20=%200.376190687;%20style%20sidec%20ball%20and%20stick;%20color%20cc4e4c;%20select%20.A:135-140%20|%20name%20peptide%2010%20fpop%20value%20=%200.030749605;%20style%20sidec%20nothing;%20color%20D3D3D3;%20select%20.A:147-154%20|%20name%20peptide%2011%20fpop%20value%20=%200.252868233;%20style%20sidec%20ball%20and%20stick;%20color%20cc7776;%20set%20mode%20all;%20select%20main%20chains;%20set%20surface%20Van%20der%20Waals%20surface;%20set%20mode%20all
select main chains
color grey
select .A:2-17
select .A:2-17 | name peptide 01 fpop value

Open a structure file

Want to use a command line:

file:///path/full.html?pdbfile=<filename>

Run command line tests

Build iCn3D,
Run node.js commands - need to find documentation

https://github.com/ncbi/icn3d/tree/master/icn3dnode

open struture + state file

want to
file:///path/full.html?pdbfile=<filename>;statefile=<statefile>

Color Keys / Legends - Atoms

Style triggers for atom color key (Color -> Atom). Structures for testing are at the bottom of the readme

General operation: When a user selects certain Style and Color options a Legend with each color as a small filled circle, and the item in a 2 or 3 column table) will be available. We can pop up a legend to start and then figure out where is should go when things are working. For example carbon would be: a gray circle Carbon.

Style (menu):
Selected Styles and Colors that make the Atom color key available are:
For proteins and nucleotides, selecting any of the below, with Color -> Atom selected, shows the atom color key
Proteins (only if the structure has protein chains):

Schematic
C-Alpha Trace
Backbone
B-Factor Tube
Lines
Stick
Ball and Stick
Sphere

Nucleotides (only if the structure has nucleotide chain):

Backbone
Lines
Stick
Ball and Stick
Sphere

Any one of the below would make an atom key available
Chemicals:

Lines
Sticks (Default)
Ball and Stick
Schematic
Sphere

Ions:

Sphere
Dot

Water:

Sphere
Dot

Color (menu):
if Style -> Chemicals -> NOT Hide & Style -> Water -> NOT Hide & Style -> Ions -> NOT Hide )

Rainbow
Spectrum
Structure
Chain
3D Domain
Residue

Any of the above Styles are set
Atom

Structures for testing:
1NAJ – DNA only – no protein
4AQD – Protein only, lots of sugars, no nucleotides
1TUP – Protein and DNA (default iCn3D structure)

Note: Proteins with sugars (glycosylated proteins) are loaded with sugar in atom coloring with the defualt Style -> Chemicals -> Sticks.

Colors for the key are in icn3d/src/utils/parasCls.js – function = this.atomColors
parasCls.js has other colors we will use later.

Build iCn3D

Get code from
https://github.com/ncbi/icn3d

Follow build instructions: https://github.com/ncbi/icn3d#building - to build working copy

Need to annotate index.html with code modifications

this will help us keep up with new versions where full.html is modified. When Jiyao added support for alpahfiold he added a new retrieve by id just after:
else if(cfg.pdbid !== undefined) {
setupViewer('pdbid', cfg.pdbid, cfg);

It's missing in our index.html