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mallen2's picture
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I downloaded the standalone version of fold.it and when i try to open a PDB file right after the program launches, it suddenly crashes. I have tried multiple files as well as re-downloading the program and trying on both a MAC and PC. Any suggestions?

beta_helix's picture
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only keep the ATOM lines in your PDB file

Rosetta has issues with all the non ATOM lines in PDB files.

If you just grep out all the ATOM lines you should be able to load any .pdb file.

ie just delete every single line that doesn't start with ATOM

mallen2's picture
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how?

how do i get into the file to delete the non ATOM lines? i have to do all of this from my own PC and am not familiar with this. a log.txt showed up in the file after saying there is probably a problem with the font file. i have a basic knowledge of computers so im not sure how to delete these lines. any help is much appreciated.

mallen2's picture
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i think i may have figured it

i think i may have figured it out. i opened the pdb file from the website, copied it, and pasted it into notepad. i then did a search and replace and removed anything that didnt start with ATOM. i then saved the file as .pdb extension and it worked! im just making sure that this is the correct way and that the protein im seeing should be the correct one

beta_helix's picture
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yes, that is the correct way to do it

a PDB file is just a text file, so you can open it in any text editor and remove every line that doesn't start with ATOM

mallen2's picture
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Thank you very much for all

Thank you very much for all of your help!

Joined: 06/25/2009
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Saving Crash

I am experiencing major problems while using the standalone version of Foldit in both MAC and Windows versions.

The system I am working on is a trimeric protein containing approximately 2k (2000) residues, a massive system.

Using the windows version in a powerful machine, I manage to perform the alterations I need, but the program crashes when I prompt to save as PDB.

As for the MAC version, I am able to save the coordinates of the whole system, but the program crashes during the modifications needed (such as using the wiggle tool).

I have frozen the protein structure and unfrozen a few residues (about 10) before wiggling in order to prevent crashing but with no success (in the MAC version).

I would appreciate any help.

Joined: 06/17/2010
Too big.

Foldit clinet can handle 300-500 residues tops. Bigger puzzle are killer.

Joined: 06/25/2009
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ok, but with the windows

ok, but with the windows client i manage to do all the work, but can't save...

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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