UPDATE: problem solved //: cannot import pdb files

Started by helen88

helen88 Lv 1

When I try to import a pdb file in Foldit Standalone, I always get the same error: "Puzzle file 0000000001.ir_puzzle.pdb not found. Please try again."
I have tried this several times and used files sourced from several different sources (all of them which show the same error). Does anyone know how to fix the error/properly import these pdb files?
Thanks! xx

UPDATE: It works now :) Huge thanks to LociOiling and bkoep! Thanks guys!

LociOiling Lv 1

I'm not sure how much help we can be, but maybe we can get someone from the Foldit team involved. Here's a little bit on how the game version works in the mean time.

In the game version, files with the "ir_puzzle" extension specify the properties of a puzzle as keyword-value pairs. The "PDB URL" keyword specifies where to get the rest of the puzzle files, and contains the URL of a zip file on the Foldit server.

The game doesn't use PDB format directly. Instead, the download package contains a file with the extension "opdb", which probably means "obscured PDB". It's a binary file, not readable by humans. A download package contains several more files, some obscured like the "opuzzle_setup" file, and some in plaintext, like the "params" file. The exact mix of files depends on the puzzle.

All these files are related by the node number on the Foldit website. So puzzle 1699 is node 2007949, which expands to https://fold.it/portal/node/2007949, it's page on the Foldit website.

Puzzle 1699 has the following setup files:


The first file, 0002007949.ir_puzzle, points to the the zip file on the Foldit server that contains the other three files. The zip file contents are named like "PUZZLE.opdb", which ends up as "0002007949.ir_puzzle.opdb" once the game client unpacks things. So the "PUZZLE" part of the name for each zipped file gets replaced by the name of the ir_puzzle file.

I have no idea how applicable all of this is to standalone Foldit, but everything ends up in the same directory as the main Foldit executable, which is foldit.exe on Windows. (This directory can get a bit cluttered as a result.)

I'll see if I can find more info on standalone. I think there were some instructions distributed a few months ago, but I'm not sure they contained this level of detail. I think that unlike a plain viewer (Jmol or Pymol), standalone Foldit may need more than just a PDB file to get started.

LociOiling Lv 1

In the previous reply, I was somewhat confusing Foldit standalone with custom contests. Custom contests involve the regular Foldit game client.

The documentation for custom contests is on the Foldit website: https://fold.it/portal/customcontests

The docs for Foldit standalone are also out there: https://fold.it/dist/external/standalone/quickstart.html

Both custom contests and Foldit standalone can work with just a PDB file, so it's not a question of needing any additional files.

Standalone has sample configurations in a zip file: https://fold.it/dist/external/standalone/examples.zip

The simplest example is "example_pdb.pdb", which involves just that one file. I'd suggest trying to import that file as a starting point.

There's a log.txt file which sometimes contains useful information about error conditions. The quickstart page suggests you'd find it as c:\FolditStandalone\log.txt on Windows.

I see there's also a UserEcho site for reporting Foldit standalone issues: https://folditstandalone.userecho.com/

Unfortunately, the UserEcho site is not really active, only 22 entries, all but one marked as being 3 years old. I don't see anything about not being able to open a PDB.

Let us know whether you have any luck. If you're still having issues, you might try shooting sending a private message to jflat06 (Jeff Flatten) via the "My Messages" link here on the Foldit website.

helen88 Lv 1

Thanks LociOiling for your feedback! I tried opening the sample configurations but it still didn't work… (including the example pdb and fasta files). The same exact error as before pops up. If I open the file up directly- not through Foldit standalone- the error: "standalone_static cannot open files of this type" shows up. For reference, I use a MacBook with OS.
However, when I use the "game" version of Foldit, everything works perfectly fine- including playing/creating contests. I'll try messaging jflat06, but let me know if you (or anyone reading this) find something new!

LociOiling Lv 1

I know there was recently a new installer for the game version on Mac, but I'm not sure how this affects the standalone version. That's about the limit of my Mac knowledge with regard to Foldit.

bkoep Staff Lv 1

That's pretty strange; I haven't heard of this before! Sometimes Foldit writes more useful debugging info in the Foldit log file. Can you share your log file?

On a Mac, this can be found in Finder, by right-clicking on the Foldit app and selecting "Show package contents." Then find the log file in Contents/Resources/log.txt.

One possibility is that the Foldit app does not have write permissions in its current location, so it is unable to create the intermediate file 0000000001.ir_puzzle.pdb from your input PDB. This usually happens when people try to run Foldit without completing installation. For example, if you unpack the Foldit installer (FolditStandalone.dmg) and then try to run the Foldit app directly from the mounted installer drive, without first copying the app into your user directory.

In this case, you might try installing Foldit in a different location on your Mac. Usually the system-wide /Applications directory is fine; but maybe you could try installing Foldit in your user applications directory at /Users/helen88/Applications (with your Mac username instead of "helen88") and try running it from there.