prolint / prolint Goto Github PK

Dear bisejdiu,

Is there any way we can store the results to the database page and restore previous results after docker reboot?

Thanks !

All the best,
John

The recent changes we made to error calculations introduced a bug when we only select contacts in the submission form.

I calculated the lipid density distribution for a protein-ligand-membrane system and when looked at the density map it shows that the protein overlaps the membrane that is not the case as my protein is embedded into the membrane. Is it a visualization artifact of the program and can I rely on the results? Please see the attached picture below. The protein should be in the white gap area completely I believe. Discussion on the problem and solution would be highly appreciated. -Lokman

As mentioned in the README, ProLint has a fully functioning and secure user-account configuration. It has been disabled because we do not want account creation to be necessary to use ProLint, but there are many advantages for enabling these features for local installations.

An obvious example would be deploying ProLint on a local network where multiple users can use the same server and have their data stored indefinitely and the ability to share results with other members within the local network. It also provides a nice feature where all results can be listed on one page (no need to keep track of submission IDs) - though the latter can be added even without accounts.

The question is should we enable and support user accounts or completely remove the code that does that from the codebase?

When densities are not selected on the submission form, but contacts are calculated, we do not show the Heatmap & Density app.
We should make it work even when densities are not calculated, similar to how it works even when there are no contacts present.

Hi,

I have problems converting my gromacs MD output to the formats required for Prolint input. Is there any example/tutorials demonstrating how to do it properly?Thanks!
All the best,
John

We are using bokeh v1.4.0 which is quite old.
We should update to bokeh v2.3.1 even though that will introduce a few incompatibilities into the code which we'll have to fix.

Calculations can be time-consuming and users may prefer to not keep tabs open and instead get notified via email when calculations are done. Adding support for email notifications would be a useful feature.

There are several developments that are only available on the webserver and have not yet been pushed to the GitHub repo.

Please use this space to comment or report any problems or issues using the ProLint webserver (prolint.ca).

Following is the error I am encountering while following the steps stated here (https://github.com/ProLint/ProLint):

Error response from daemon: Error when allocating new name: Conflict. The container name "/prolint-web-1" is already in use by container "1c4a068a20e6c0bac6dbf221cc6612c67ba43c5bf3b8729fb554a5cac687acb5". You have to remove (or rename) that container to be able to reuse that name.

I was wondering how can I remove/rename the container. Any directions are highly appreciated.

Please use this space to report any problems when installing the software.

Errors are already calculated but currently, they are not stored and therefore not visualized.
When there are multiple copies of a protein in the system it would be useful, however, to also visualize errors and add support of the visualization apps to display them.

The PENDING state currently means either that the submission has been put on a queue or that the calculations have started.
It would be much better to have separate states for these two events.