- This topic has 2 replies, 2 voices, and was last updated 9 years, 2 months ago by Anonymous.
September 24, 2014 at 10:02 am #2006Anonymous
I am dealing with a PDB file missing some residues. I think I should clean it by clean_pdb.py of Rosetta or cleanATOM of PyRosetta.
In Rosetta, the clean_pdb ignores the missing positions and renumber all the residues from 1 to the end regardless of the missing gap.
In PyRosetta, the missing gap can still be remained.
Can I ask can I get the result similar to cleanATOM by using Rosetta’s clean_pdb.py? I think I should clean the PDB first, then do loop modeling for the missing residues. Is that correct?
Thank you very much.
September 26, 2014 at 10:41 pm #10317Anonymous
I don’t think there’s an option in the distributed clean_pdb script not to renumber the residues.
Now-a-days, though, Rosetta itself is pretty good at cleaning up PDBs if you pass the appropriate options. I myself tend to use Rosetta directly, rather than relying on an external script. Try something like the following commandline:
main/source/bin/score_jd2.linuxgccrelease -ignore_unrecognized_res -ignore_zero_occupancy false -out:pdb -s FILE_TO_CLEAN.pdb
This hopefully will result in a FILE_TO_CLEAN_0001.pdb file which represents what Rosetta thinks the PDB looks like.
Sometimes it doesn’t quite work, but usually in those cases it’s a quick fix with a search/replace or deleting lines with a text editor.
(Edit: fixed commandline)
September 24, 2014 at 7:34 pm #10322Anonymous
(I do not know why but it seems that recently I always encountered error when I submit a comment in this forum. It turned out to be okay when I re-edit the comment)
Hi R Moretti,
It really works, so amazing!
A new file of file_0001.pdb (and score.sc) was created, 1) with full hydrogens, 2) without filling the missing residues to re-number, 3) with score comment in the end
So I delete the score in the end to get a clean PDB file.
Thank you very much.
(The first trial did generate any file though the prompt in the terminal seemed to be okay. So I tried again and got those files. But anyway, the problem has been solved.)
(Just to correct, it is score_jd2 instead of sdore_jd2)
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