Uploading to server fails without error output

i’m trying to submit some jobs but after uploading the files I got the blank form back without error messages.
I cleaned up all PDBs using PDBtools, all with unique chain identifiers, <99999 atoms <9999 residues (i’d like to attach the files but as new user I can’t…). I checked the restraint file if they correspond, the order, the format etc… I tried almost everything now. Any idea of what went wrong? would be good to have an error message output when something is wrong to know where to look.



How large are your molecules in terms of number of residues?

PS: Did you try one of our tutorial and does it work for you?

E.g.: https://www.bonvinlab.org/education/Others/disvis-webserver/

the fixed molecule has 11274 residues (98032 atoms, so no weird naming that i knew they mess up), the scanning one 410 (3638 atoms). Do i need to remove residues from the fixed pdb?

And to answer to the next question, yes, i did try the tutorial files a they work (P.S. i already removed quite some chains from the Fixed molecule… if i have to remove more this can be an issue for the significance of the run unfortuantely)

P.S. i fwd the files yesterday at the email address of DisVis support.

This is huge!!! I am afraid it will not work…
If you have cross linking data for example, can’t you trim down your molecule to something more reasonable?

Your smaller molecule clearly won’t be sampling the entire surface.

What kind of distance restraints to you have?

ok, i see the problem. Maybe would be a good idea to know that there are these limitations :wink:

I already trimmed down to the chains for which i also have distance restraints, but these are also repeated multiple times in the complex, which originally is a dimer of hetero-dimers (of ~18 chains each). I wanted to use disvis to sample the meaningful ones, but i guess i’ll have to trim down more than that (already removed about half of the chains, the smaller ones though).

So any precise limit in term of residues i can submit per single PDB?

I have ~130-160 distance restraint from cross-linking MS (6 to 33 A)

You can always run a local version of DISVIS if you have plenty of CPUs and memory :slight_smile:

It is freely available from https://github.com/haddocking/disvis

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Thank you for the suggestion, i will try, but i’m wondering if something changed since few months ago i submitted a run with the PDB #5XNL (9364 residues, 98986 atoms, 56 chains) and it worked. Now with a smaller model it does not ( i trimmed down again to 8542 atoms, 30 chains, and ~75000 atoms). It’s just a bit annoying to waste time in trying to adapt your scanning chain to stick to some limitations which are not specified (# atoms? chains? residues?).
But thanks for your help anyway, hopefully in the next version (if any) a more informative output error message will be included.

Hi Pascal

We dig into the log files to figure out the problem. The only error we could find that day is:

> 2020-06-09 09:19:53,388 - views.py:166 - INFO - Could not validate form {'restraints_file': ['TBL file wrongly formatted.\nERROR: Could not parse the TBL file at line 1\n(Offending Line: e 7 CA A 215 CA 6 35) \n(Example Valid Line: A 18 CA F 27 CB 10.0 20.0)']}

Not sure if this is your submission though.

We will try to improve the error reporting.

Thanks for the reporting, yes this looks definitely my submission.
Seems that could be the lower case lettering, or the format of the distance (even though in the example TBL of the tutorial is without “.0” decimal values). I actually tried both formats for the distance values. It sounds weird however that the issue is in the upper/lower case chains names, as i already submitted PDBs with lower case letters.

Thank you, i’ll keep you posted if i manage to get a run going trough :wink: