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dsehnal / LiteMol

A library/plugin for handling 3D structural molecular data (not only) in the browser.
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how to load my own channels data in LiteMol #70

Open jingyile opened 3 years ago

jingyile commented 3 years ago

Hello! I am working on implementing the molecular viewer "LiteMol" on my html webpage. The plugin is working great in examples/Channels. I found that the version of mole in data.json is 2.5.17.9.28, but my mole version in my own data.json is 2.5.17.4.24.(I found the current version of mole is 2.5.17.4.24 too, http://webchem.ncbr.muni.cz/Platform/App/Mole) I can't display my own channel data. I guess this is a version problem, but I don't sure. I desperately need your help! please!

my own data.json:

image

your data.json:

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this is the issues:

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dsehnal commented 3 years ago

Hi,

it seems like your output doesn't contain the geometry of the channels. I don't remember it from the top of my head, but there is an option that adds that to the output.

David

jingyile commented 3 years ago

Thank you very much for your reply！ Please take a look at this link, I want to know the source of data.json. I produced this file by the command line version of MOLE, but the structure of the data is different from yours. So I want to know the version of MOLE that you used, or what adjustments can I make to display my data. This problem has bothered me for many days. in a word, I want to display my own channel data, my data.json is produced by the MOLE(version:2.5.17.4.24) please help me. thank you very much! data.json.zip

and I use LiteMol-example.js that from (https://litemol.org/Examples/Channels/).

image
dsehnal commented 3 years ago

I am sorry, but this is more involved than I have time to help with now so you will have to figure out things on your own. I no longer develop LiteMol as I've shifted my efforts to develop Mol*. Writing an extension for Mol* that can display channels might be a good thing for community do. Do you think you can help with that?

jingyile commented 3 years ago

I am honored to receive your suggestions. I also think this is a good idea. But I am a student, and i don’t have much time to participate in it now. I must try to display channels by LiteMol first. if I hava enought time to do it in the future, I'm happy to try it.

By the way, do you have a mole of version 2.5.17.9.28? I am looking for it. I can't find it in http://webchem.ncbr.muni.cz/Platform/App/Mole. Thanks!

dsehnal commented 3 years ago

That version isn't available online and it won't help you achieve your goal. The purpose of the LiteMol demo was to show how to do some custom visualizations in LiteMol, not for it to serve as a working app to display any channel.

As an alternative, can you compute your channels in https://mole.upol.cz/ ? You can then link to a result with the channels displayed, for example https://mole.upol.cz/online/fzSWlM4cWEqUmJ3EyRy7Qw/1 .

jingyile commented 3 years ago

hahah! I found that this output file(data.json) really has nothing to do with the version. I happened to try this online version today. I also think I can achieve the same effect through the online version. I will discuss with my mentor. Your reply is very useful！ thank you!