Comments (5)
Hi, thanks for your report.
Yes, I think NGL should use the author supplied names when possible. It is currently not coherent, e.g. auth_seq_id
is used but not auth_asym_id
. I will look into changing it. There needs to be a fallback if auth_asym_id
is not there as it is not required, but label_asym_id
is required. Moreover, some data in the mmcif file is linked by the label_asym_id
(_pdbx_struct_assembly_gen.asym_id_list
), so that field need to be read anyway.
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Hi, thanks for your prompt reply.
I put in a dirty hack in my copy for now, to allow my development to continue. I'm not sure if or when I will run into issues because of that. I look forward to your proper fix whenever you get a chance. Next on my list is to extend it's API to support a more convenient to me syntax of custom coloring residues. I can do a pull request for that, but I understand if you don't accept it. That's the beauty of JavaScript, I don't need anything officially added to do it. I can extend at run time.
This project is a lifesaver. I have been using Jmol, but Java is dead. Chrome dropped support, Firefox will be dropping Java support soon, and may other browsers don't have Java support either. JSmol is too slow for large molecules without WebGL. Unless they get serious about making their WebGL version work, NGL Viewer is the best option for sure.
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Fixed this in commit 8afe455. Testing appreciated. With that auth_asym_id
is used instead of label_asym_id
as the chainname
. Additionally I made sure that label_asym_id
in _pdbx_struct_assembly_gen.asym_id_list
and in other places is mapped to the corresponding auth_asym_id
during parsing.
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Next on my list is to extend it's API to support a more convenient to me syntax of custom coloring residues. I can do a pull request for that, but I understand if you don't accept it.
Please do make a PR or open an issue. I am very happy to discuss the API!
from ngl.
OK great. I'm working on some other parts of my program right now. When I get back to NGL, I will switch to your dev version, test your changes, and develop my api feature.
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Related Issues (20)
- dispose() method leaves part of the old representation when changing model HOT 2
- Incorrect behavior when changing opacity for a separate pocket HOT 3
- Should threejs be changed to a peer dependency? HOT 2
- change color of specific residue HOT 2
- getAtomSetWithinSelection and getAtomSetWithinGroup in several files HOT 4
- info in tooltip HOT 2
- Mass in .pdb files HOT 2
- Focus camera on selection
- Allow more export of components HOT 4
- Why is the effect after superposition not as good as before superposition HOT 1
- Export .pdb file HOT 2
- Question: How to save and restore transformation?
- Funnel like shape
- Multi-touch zoom with multiple NGL instances
- Show connections in two difference files HOT 4
- Hiding non-polar hydrogens HOT 1
- MeasureRepresentation between non-atoms HOT 2
- displaying hydrogens as ligands HOT 1
- Select the entire molecule by clicking on its atom HOT 1
- Regressions
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