rudoroemer / pdb2movieweb Goto Github PK

Hi Sam,

can you please check the formatting of the privacy statement in the online-patch branch and then merge into the master? Thanks.

The final download link should always contain

[1] the input file of the submission parameters,
[2] the original .pdb file
[3] the .py file, if there was one submitted.

This would then mean that users have a fully self-contained output link, i.e. such that all the information needed to check the output (and redo) is contained in that single download.

Three changes to the report (sample given below):

[1] include the submission.txt header

[2] change the email address to something like [email protected]

[3] Give the name of the submitted file instead of "unnamed.pdb".

From admin [email protected]

file: unnamed.pdb
python file used: N/a
resolution: 1920
combi: 1080
multi: 1
waters: 0
threed: 0
confs: 0
freq: 2000
step: 100
dstep: 0.1
Keep list: 0.01
Modes: NULL
Cutoffs: 7
Date Submitted: 2.0

Your User Reference Code: 27

The "data submitted" is formatted wrongly and overwrites the reference code.

Your request for a PDB2Movie calculation has now started execution. You will receive a final email notification with a download link once the job has finished.
...

Your request:

file: 2B5E_FH.pdb
python file used: 0
resolution: 640 480
combi: 0
multi: 1
waters: 0
threed: 0
confs: 2000
freq: 100
step: 0.1
dstep: 0.01
Keep list: NULL
Modes: 7
Cutoffs: 2.0
**Date Submitted: 10

Your User Reference Code: May**

It would be good to have the version of the code available on the server. I would suggest something simple such as just the date of the u0pload to the servers (via buddy). buddy can simply "sed" something like a "PUSHDATE" string on the .html files with the actual date. I think github does not readily make a version number available (but maybe it does).

We need to move from Sam's user to a general project user (hopefully called pdb2movie). This is already in discussion with ITS via helpdesk request reference INC0677291 on 21-05-2018 16:26:23 BST.

As is shown below, the download link in the present advem version is broken/incomplete.

-Rudo

Your request for a PDB2Movie calculation has now finished execution. A download link is given below.
This link will normally remain active for 7 days but can also be removed by the system earlier. It is your
responsibility to start the download as soon as possible.

Your parameters are again appended below.

Please note that this service uses low priority compute cycles at the Scientific Computing Research Technology Platform
at the University of Warwick. The service is provided for free at the moment based on a low volume of such requests.

If you wish to use the service more often, please get in touch as explained on our PDB2Movie web pages.

If you use the results of this calculation in a commercial and/or academic output (such as a patent or a paper), please
remember to acknowledge our two papers

[A] "Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses"
E. Jimenez-Roldan, R. Freedman, R. A. Römer, S. A. Wells
Physical Biology 9, 016008-12 (2012)
http://dx.doi.org/doi:10.1088/1478-3975/9/1/016008

[B] "The dynamics and flexibility of protein disulphide-isomerase (PDI): predictions of experimentally-observed domain motions"
R. A. Römer, S. A. Wells, J. E. Jimenez-Roldan, M. Bhattacharyya, S. Vishweshwara and R. B. Freedman
Proteins: Structure, Function and Bioinformatics 84, 1776-1785 (2016)
http://dx.doi.org/10.1002/prot.25159

Your request:

file: 3F8U_FH.pdb
python file used: 0
resolution: 1920
combi: 1920
multi: 1080
waters: 1
threed: 0
confs: 0
freq: 2000
step: 100
dstep: 3F8U_FH.pdb0
Keep list: 3F8U_FH.pdb1
Modes: 3F8U_FH.pdb2
Cutoffs: 3F8U_FH.pdb3
Date Submitted: 3F8U_FH.pdb4

Your User Reference Code: 3F8U_FH.pdb5
Download Link: /download/1aae6b8133940faf00ddc5afbb27016771de71f.tar.gz

The number of maximum daily request does not seem to reset.

I just submitted three jobs, but always get told "8/10 of my quota". The counter does not seems to work nor to reset.

Download Link: https://advid.lnx.warwick.ac.uk/download/b002dd2f2a3d936aa897a143552b33e01c84cdc0.zip

The link still points to advid.lnx but should point to pdb2movie.warwick.ac.uk. Same probably for the test server where the correct link should be to pdb2movie-test.warwick.ac.uk

due to the new DESKTOP2018 on the SC RTP, there may be a new queuing system integration needed

Positive and negative directions should be combined into a single video file. This is implemented, but at present the combined movie does not seem to contain both directions, it seems to be the positive direction only.

contents of pdb_des and pdb_tmp are not emptied upon request cancellation or completion, despite the rm commands being there. When manually ran after the process, this is successful. Debugging required.

It would be good to have three more entries in the "review.html" list of jobs, namely a column on whether the job was submitted/processing/completed. I envisage something like

submitted processing completed
20/04/2018 21/04/2018

for a jobs that is not yet completed.

This affects the daily resets, not an issue during testing, especially since the job increment is disabled during this period.

When reviewing a job and removing it, the data the the newly added comment text is not deleted. This is only corrected upon a reload.

When sanity-checking .pdb files, we disallow the apostrophe ('). However, many .pdb files use the ' genuinely in comments and more. We hence should re-allow its use.

For copyright and compatibility reasons, we need to move the standard renders from PyMOL to VMD

Amazing work!

We could add the RCD .ps files as well as the .log files. For security reasons, the .log files should not contain any user-related file directories.

Hi,

please make an option in the submit tab to also download all the conformer files (.pdb) that are being used to create the movies. People might very well want to use these for their own analysis.

Somehow the movies made by PDB2MovieWEB do not play on the CentOS/MATE installation of the 2018 SC-RTP Desktop. Perhaps this is just an issue of the codec used?

I quite often find myself wishing there was a simple text box o=in the submission form which I could use to label my PDB2Movie jobs (with a label, a number, etc.). Something like:

2BE5, now with correct colors, low resolution for main web page.

currently no parsing is done on output video files on any live version of PDB2MovieWeb. Needs work.