unable to use custom .pdb files as hoped for template

[CameronWeller]

Expected Behavior

hopefully being able to use a .pdb with some small modifications

Current Behavior

I removed the chains of a complex of my protein (the only crystal structure we have right now is the protein in complexes) pdb ID 4nzr. After removing the deleting the extraneous chains in Chimera then exporting/saving as .pdb it was unable to be used as a .pdb.

Steps to Reproduce (for bugs)

described in current behavior

Please make sure to reproduce the issue after a "Factory Reset" in Colab. If running locally ypdate you local installation colabfold_batch to the newest version. Please provide your input if you can share it. input for the sequence is :

TNLVNQSGYALVASGRSGNLGFKLFSTQSPSAEVKLKSLSLNDGSYQSEIDLSGGANFREKFRNFANELSEAITNSPKGLDRPVPKTEISGLIKTGDNFITPSFKAGYYDHVASDGSLLSYYQSTEYFNNRVLMPILQTTNGTLMANNRGYDDVFRQVPSFSGWSNTKATTVSTSNNLTYDKWTYFAAKGSPLYDSYPNHFFEDVKTLAIDAKDISALKTTIDSEKPTYLIIRGLSGNGSQLNELQLPESVKKVSLYGDYTGVNVAKQIFANVVELEFYSTSKANSFGFNPLVLGSKTNVIYDLFASKPFTHIDLTQVTLQNSDNSAIDANKLKQAVGDIYNYRRFERQFQGYFAGGYIDKYLVKNVNTNKDSDDDLVYRSLKELNLHLEEAYREGDNTYYRVNENYYPGASIYENERASRDSEFQNEILKRAEQNGVTFDENIKRITASGKYSVQFQKLENDTDSSLERMTKAVEGLVTVIGEEKFETVDITGVSSDTNEVKSLAKELKTNALGVKLKL

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

2022-08-01 18:41:52,309 Found 7 citations for tools or databases

ValueError Traceback (most recent call last) in () 52 stop_at_score=float(100), 53 prediction_callback=prediction_callback, ---> 54 dpi=dpi 55 )

1 frames /usr/local/lib/python3.7/dist-packages/colabfold/batch.py in mk_hhsearch_db(template_dir) 249 if res.id[2] != " ": 250 raise ValueError( --> 251 f"PDB contains an insertion code at chain {chain.id} and residue " 252 f"index {res.id[1]}. These are not supported." 253 )

ValueError: PDB contains an insertion code at chain H and residue index 31. These are not supported.

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used
• If you run it on a local system. Please add the server specifications
• Operating system and version: this is being run pdb files used.zip on google colab

[SamFreemanFox]

Did you ever manage to resolve this? Just run into the same issue

[SamFreemanFox]

Have found a work around to the error. It is due to insertion codes within the PDB file itself which can be removed from the file in a text editor. I do not know the impact of removing the insertion codes but the model opens in Chimera identically to the unedited version.

ATOM 11918 CZ PHE D 100 -6.852 76.356 -23.289 1.00107.94 C ATOM 11919 N ARG D 100A -9.676 74.726 -19.958 1.00105.71 N ... ATOM 11970 CE MET D 100H -8.264 83.348 -19.494 1.00107.93 C ATOM 11971 N ASP D 101 -11.329 81.237 -14.804 1.00107.41 N

Look through the text file and delete any letters in column 27 in the section of the file that looks like the above and it should then run.

[CameronWeller]

beautiful ! I am no longer working on AF right now but this is super helpful to know!

On Mon, May 15, 2023 at 5:51 AM SamFreemanFox @.***> wrote:

Have found a work around to the error. It is due to insertion codes within the PDB file itself which can be removed from the file in a text editor. I do not know the impact of removing the insertion codes but the model opens in Chimera identically to the unedited version.

ATOM 11918 CZ PHE D 100 -6.852 76.356 -23.289 1.00107.94 C ATOM 11919 N ARG D 100A -9.676 74.726 -19.958 1.00105.71 N ... ATOM 11970 CE MET D 100H -8.264 83.348 -19.494 1.00107.93 C ATOM 11971 N ASP D 101 -11.329 81.237 -14.804 1.00107.41 N

Look through the text file and delete any letters in column 27 in the section of the file that looks like the above and it should then run.

— Reply to this email directly, view it on GitHub https://github.com/sokrypton/ColabFold/issues/279#issuecomment-1547802415, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE3GRYORZYWELSTBXNKZRDDXGIRFDANCNFSM55IQSOKA . You are receiving this because you authored the thread.Message ID: @.***>

--

• Cameron Weller

[Masterchiefm]

Have found a work around to the error. It is due to insertion codes within the PDB file itself which can be removed from the file in a text editor. I do not know the impact of removing the insertion codes but the model opens in Chimera identically to the unedited version.

ATOM 11918 CZ PHE D 100 -6.852 76.356 -23.289 1.00107.94 C ATOM 11919 N ARG D 100A -9.676 74.726 -19.958 1.00105.71 N ... ATOM 11970 CE MET D 100H -8.264 83.348 -19.494 1.00107.93 C ATOM 11971 N ASP D 101 -11.329 81.237 -14.804 1.00107.41 N

Look through the text file and delete any letters in column 27 in the section of the file that looks like the above and it should then run.

It worked!