"Downloading" files within my machine

[Raiyan-Rizwan]

Hi,
I noticed that the API allows download via url, but what would I do if I am to use a pdb file within my machine's file system?

[sbittrich]

Hi @Raiyan-Rizwan,

Please see #18 for details.
Local files aren't supported because the resulting MVS file wouldn't work on other machines. You can always upload your data to S3, Google Drive, Dropbox, ...

Best,
Sebastian

[Raiyan-Rizwan]

Good Afternoon,
So I am using Google Drive as a web platform to host the pdb files I am going to visualize on Molstar. I get the file from google drive and produce the download link using the following code:

def get_drive_download_link(drive_url):
"""
Converts a Google Drive sharing URL into a direct download link.
"""
file_id = drive_url.split('/')[-2]
return f'https://drive.google.com/uc?export=download&id={file_id}'

Then I run the download link through the builder(made using molviewspec built in functions). However, I get the following error. Do you have any suggestions for fixing this error?

Thanks

[sbittrich]

Indeed, thanks for giving this a try. We'll look into this, though I'm not sure if this is fixable in Mol*/MolViewSpec or if this is a more general issue with how Google Drive decides to share files.

[Raiyan-Rizwan]

Good Afternoon,
Were you guys able to get to what is causing the issue? Please let me know.

Thanks

[sbittrich]

@midlik Do you think this can be addressed in the Mol* code or is this a limitation of Google Drive?

[midlik]

Hi, this looks as a CORS problem.
So there is no way of addressing this in Mol*.
The files must be served with CORS enabled (and unfortunately I don't think GoogleDrive allows this, S3 might allow you to enable it).

[midlik]

If you have no possibility of hosting those structure files with CORS enabled, you can still use relative URL and pack you MVSJ + structure files into a MVSX file (https://molstar.org/mol-view-spec-docs/#mvsx). Something like this:

builder.download(url='./my-structure.cif')
...
builder.save_state(destination='example.mvsj')

import zipfile
with zipfile.ZipFile('example.mvsx', mode='w') as z:
    z.write('example.mvsj', arcname='index.mvsj')
    z.write('my-structure.cif', arcname='my-structure.cif')

[Raiyan-Rizwan]

It worked with S3. Thanks!

[Raiyan-Rizwan]

The following is an example from the code you guys provided within your Python Collab Notebook:

builder = mvs.create_builder()
structure1 = (
builder.download(url="https://files.wwpdb.org/download/1oj6.cif")
.parse(format="mmcif")
.assembly_structure()
)

1st structure colored in orange

structure1.component(selector='polymer').representation(type='cartoon').color(color='#e19039')
structure1.component(selector='ligand').representation(type='ball_and_stick').color(color='#eec190')

structure2 = (
builder.download(url="https://files.wwpdb.org/download/5mjd.cif")
.parse(format="mmcif")
.assembly_structure()
# move these coordinates to align both structures
.transform(
rotation=[-0.39652203922082313, 0.918022802798312, 0.002099036562725462, 0.9068461182538327, 0.39133670281585825, 0.1564790811487865, 0.14282993460796656, 0.06395090751149791, -0.9876790426086504],
translation=[-17.636085896690037, 7.970761314734439, 88.54613248028247]
)
)

2nd structure colored in blue

structure2.component(selector='polymer').representation(type='cartoon').color(color='#4b7fcc')
structure2.component(selector='ligand').representation(type='ball_and_stick').color(color='#9cb8e3')

print(builder.get_state())

I have used a similar structure in my code to represent two different protein structures together. However, When I directly convert the JSON form of the state into a URL and use it on the web, I get a "URI too long" error. However, you guys were successfully able to visualize it. May I ask what technique you guys used for the URL conversion? It would be very helpful for me.

Thanks

[Raiyan-Rizwan]

Hello,
Can you guys please let me know what technique you used to convert the output of builder..get_state(), which is in JSON format to URL in this specific case? Would be very helpful.

Thanks

[midlik]

Hi Raiyan,
I understand that your question is about using the mvs-data URL parameter. Unfortunately, URL length is limited in most browsers and only very simple MVS views fit into this limit. If you have a more complex view, you'll have to use a different method of sharing, e.g. host the file somewhere and use the mvs-url parameter.

Find some documentation here: http://molstar.org/mol-view-spec-docs/mvs-molstar-extension/

[Raiyan-Rizwan]

Thank you guys for the response to my last question. I was able to host the file on Amazon AWS and view the structure.

I do have one more issue where I initially specify in my code that the protein(cluster) is to be represented by type "ball_and_stick". However after I visualize it, it appears in type "cartoon" as I posted right below:

Then when I manually switch the type from "ball_and_stick" to "cartoon" and then back to "ball_and_stick", that's when it shows the structure in the proper "ball_and_stick" format as I posted below:

So why doesn't it show the structure in the proper "ball_and_stick" format directly from my code? I am pretty sure I am setting the representation parameter to type=ball_and_stick correctly. Can you please check if this is a bug on your end?

Thanks a lot.

[midlik]

Hi,
looking at the pictures, there are both ball-and-stick.
The difference is that the first one uses MolViewSpec parameters (larger ball size) while the second one uses default Molstar parameters for ball-and-stick.
MolViewSpec parameters were selected to make typical structures look nice (see attached images), while your data are just a bunch of points.

In the current MVS implementation, we don't have any mechanism to specify the parameter values, unfortunately.