Change the number of residues on pdb file!

[Anonymous]

I am a new Rosetta user. I have some problems because I don not understand about how Rosetta work exactly. With docking, I have to prepare a file pdb have 2 chain (in my case :1 enzyme and 1 peptide), and enzyme have to have residues number start at 0, right? how I can change the number of residues on pdb file?
I have to prepacked pdb file before docking, right?
Thank you so much.

[Anonymous]

You don’t *need* to renumber the PDB in most cases. Rosetta can (often but not always) handle PDB files which start at arbitrary numbers, as well as PDB files which jump around in numbering and have gaps. (And depending on what you’re doing, repeats can be handled fine too, as long as they’re not consecutive.)

The reason you see recommendations on renumbering your proteins in Rosetta is that Rosetta has an internal numbering system (“pose numbering”) which starts from 1 (not zero) at the first residue of the first chain, and continues increasing for each additional residue, ignoring missing residues and continuing on through multiple chains. This pose numbering is exposed to the user through various file formats and input usages, so it’s important to know the translation between pose numbering for your protein and the pdb numbering. Depending on what you’re doing it can be a pain to translate, so if you make the PDB numbering match the pose numbering, your life gets easier.

There are a number of scripts that have been made to do the renumbering as well as various cleanup tasks. (rosetta/tools/protein_tools/scripts/clean_pdb.py is one such script – run with the “-h” option to get usage information.) But honestly, I’d recommend just using Rosetta as your renumbering tool. You’ll get the most accurate knowledge of how Rosetta will read in your protein as well as any modifications/alterations it will do. You can use the score_jd2 application for this:

score_jd2.default.linuxgccrelease -renumber_pdb -ignore_unrecognized_res -s input.pdb -out:pdb

This will output a input_0001.pdb file, renumbered according to pose numbering, with hydrogens and missing sidechains added and repacked, and with any residues that Rosetta doesn’t understand or cannot place (e.g. because of zero occupancy) removed. Open it up in As a bonus, the PDB will have a per residue score table at the bottom, so you can see if there are any residues which have major clashes or scoring issues.

Regarding prepacking, yes, you probably want to do some sort of relaxation preparation prior to the main docking protocol. Usually there will be a recommended preparation protocol associated with the docking protocol. For the standard protein-protein docking protocol (https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d0/de4/docking_protocol.html) the documentation for the prepacking protocol is here: https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/de/d69/docking_prepack_protocol.html

[Anonymous]

Following your suggestion, I am using

score_jd2.default.linuxgccrelease -renumber_pdb -ignore_unrecognized_res -s input.pdb -out:pdb

to renumber my pdb files. Is there a way to prevent the score table at the bottom from being written to the clean pdb file? I am working with many structures and this table increases the size of the files significantly.

Thanks.

[Anonymous]

As jwillis mentions in another thread (https://www.rosettacommons.org/node/3998), there isn’t any flag currently to turn off the scoring table in PDB output and you may want to use the clean_pdb script instead. Alternatively, you could try -out:pdb_gz to save space by outputting them as gziped files, and/or -score:weights empty to still get the table, but without most of the entries.

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